Protein Data Bank Contents Guide:

Atomic Coordinate Entry Format Description

Version 2.1 (draft), October 25, 1996

Example

Preface

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data.

Entries conforming to this format description have the following remark within them:

       REMARK   4 XXXX COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996

Entries released after October 25, 1996 will comply with this format. Conversion of older entries to this format will begin in the fall of 1996.

This Contents Guide was prepared through the efforts of all PDB staff members: J. Callaway, M. Cummings, B. Deroski, P. Esposito, A. Forman, P. Langdon, M. Libeson, J. McCarthy, J. Sikora, D. Xue; and especially E. Abola, F. Bernstein, N. Manning, R. Shea, D. Stampf, and J. Sussman. This document also included significant contributions from the scientific community whose members continually send us suggestions and comments regarding the contents and format of PDB entries.

The PDB is supported by a combination of Federal Government Agency funds and user fees. Support is provided by the U.S. National Science Foundation, the U.S. Public Health Service, National Institutes of Health, National Center for Research Resources, National Institutes of General Medical Sciences, National Library of Medicine, and the U.S. Department of Energy under contract DE-AC02-76CH00016.


Table of Contents

Preface

Table of Contents

1. Introduction

  • Purpose of this Document
  • What's New in Version 2.1
  • What's New in Version 2.0
  • Changes to PDB Format 2.0 Being Proposed on October 25, 1996
  • Changes to PDB Format and to the Contents Guide
  • Basic Notions of the Format Description
  • Record Format
  • Types of Records
  • Order of Records
  • Field Formats

2. Title Section

  • HEADER
  • OBSLTE
  • TITLE
  • CAVEAT
  • COMPND
  • SOURCE
  • KEYWDS
  • EXPDTA
  • AUTHOR
  • REVDAT
  • SPRSDE
  • JRNL
  • REMARK
  • REMARK 1
  • REMARK 2
  • REMARK 3
  • REMARK 4 - 999

3. Primary Structure Section

  • DBREF
  • SEQADV
  • SEQRES
  • MODRES

4. Heterogen Section

  • HET
  • HETNAM
  • HETSYN
  • FORMUL

5. Secondary Structure Section

  • HELIX
  • SHEET
  • TURN

6. Connectivity Annotation Section

  • SSBOND
  • LINK
  • HYDBND
  • SLTBRG
  • CISPEP

7. Miscellaneous Features Section

  • SITE

8. Crystallographic and Coordinate Transformation Section

  • CRYST1
  • ORIGXn
  • SCALEn
  • MTRIXn
  • TVECT

9. Coordinate Section

  • MODEL
  • ATOM
  • SIGATM
  • ANISOU
  • SIGUIJ
  • TER
  • HETATM
  • ENDMDL

10. Connectivity Section

  • CONECT

11. Bookkeeping Section

  • MASTER
  • END

Appendix 1: Symmetry Operations

Appendix 2: Coordinate Systems and Transformations

Appendix 3: Atom Names

  • Amino Acids
  • Nucleic Acids

Appendix 4: Standard Residue Names and Abbreviations

  • Amino Acids
  • Nucleic Acids

Appendix 5: Formulas and Molecular Weights For Standard Residues

  • Amino Acids
  • Nucleotides

Appendix 6: Field Formats

Appendix 7: Order of Records


1. Introduction

Purpose of this Document

The PDB Contents Guide gives a complete and concise description of the contents of PDB coordinate entry files. This document will be helpful to several communities, assisting depositors in preparing their entries for deposition, guiding software and information resource developers, and helping users of PDB to understand the contents of coordinate entries. Finally, this format description is crucial in the effort to produce CIF-compliant data files from PDB entries.

What's New in Version 2.1

List of changes/enhancements to PDB format as found in Contents Guide Version 2.1.

* MODRES records appear immediately following SEQRES. (The order was incorrectly stated in Version 2.0.)
* REMARK 3 has a new X-PLOR template to reflect the changes introduced by the recent release of X-PLOR(online)3.843.
* REMARK 3 will use the word NONE (for the attribute in the value-attribute pair) when the attribute is not applicable or when analysis options were chosen such that a value was not calculated. NULL will continue to be used to represent values not supplied by the depositor.
* COMPND and SOURCE have a few additional tokens.
* Some examples are enhanced, a few have been added.
* Language of the text has been improved in some places to help clarify the format.

What's New in Version 2.0

List of important changes/enhancements to PDB format as found in Contents Guide Version 2.0.

* Columns 71 - 80 now contain data. They previously contained the PDB ID code and record serial number. These items may be generated using scripts available from the PDB.

Changes to ATOM/HETATM Records

* A segment identifier has been added to the coordinate records in columns 73 - 76. This allows unambiguous identification of regions of the chains and the relationship between them by specifying segments of molecules.
* The element symbol and charge now appear in columns 77 - 80 of the coordinate records.
* When temperature factors are provided, the tempFactor field (columns 61 - 66) always contains the isotropic B value, even when ANISOU records are provided.
* Insertion codes (column 27) are now defined as being alphabetic only.

Changes to Other Records

* HELIX records now contain the length of the helix in columns 72 - 76.
* SSBOND records now state the symmetry operation needed to generate one of the residues of the disulfide bond, if necessary.
* Footnotes (FTNOTE) have been dropped.
* In CRYST1 records:
         - The full international Hermann-Mauguin symbol is used, 
           e.g., P 1 21 1 instead of P 21. 

         - For a rhombohedral space group in the hexagonal setting, 
           the lattice type symbol used is H.

* A number of record types which previously contained free text have been restructured as follows:
         - "Keyword: value" pairs have been introduced in certain records   
           such as COMPND and SOURCE to allow easier parsing.

         - EXPDTA has been expanded and now appears in every PDB coordinate 
           entry.

         - REMARK records have been restructured to allow easier parsing    
           and to bring more organization to these records.

New Record Types Added

* TITLE
* CAVEAT
* KEYWDS
* MODRES
* DBREF
* SEQADV
* HETNAM
* HETSYN
* LINK
* HYDBND
* SLTBRG
* CISPEP

For details on each of these changes, see the section of the associated record type in this document.

Changes to PDB Format 2.0 Being Proposed on October 25, 1996

A number of changes are being proposed to the existing data format. We are presenting these changes here for consideration. In accordance with PDB's Format Change Policy, there will be an open sixty-day discussion period during which we will entertain comments and suggestions regarding these changes. Send comments to Enrique Abola (abola1@bnl.gov) or to Nancy Manning (oeder@bnl.gov). Discussion on the PDB Listserver is encouraged as well.

Changes being proposed here, if adopted, will not appear in released entries before March 31, 1997. A public announcement will be made some weeks prior to their appearance in released entries.

1. Hydrogen Atom Names in Amino Acids

Methylene hydrogen atoms will be labeled as 2HX and 3HX where X is the remoteness indicator of the atom. For example, hydrogen atoms attached to C beta of an amino acid will be named 2HB and 3HB. Our current convention is to name these 1HB and 2HB. This change will make PDB more compliant with IUPAC recommendations.

2. Space Group Symbol for Monoclinic Crystals

The use of the shortened Hermann-Mauguin symbol for monoclinic crystals will be reinstated. This will be applied to crystals in the standard b-unique cell setting. Thus the space group symbol P 21 will be used instead of P  1  21  1. Crystals using other settings will be designated with the full international Hermann-Mauguin symbol (e.g., P  21  1  1).

3. Representation of Modified Nucleic Acid Residues

Modified nucleic acids will be represented using the same rules that are used by the PDB for representing modified amino acids. We will assign a unique three-letter code for modified residues. For example, we will use BRU for brominated uridine rather than +U. In addition, all atoms belonging to the residue will be grouped together in the coordinate records. Our current practice is to list atoms that modify nucleotides after the TER record.

Changes to PDB Format and to the Contents Guide

When a change is made to PDB format, the format version number, as found in the entry and in this Contents Guide, will be incremented to the next whole number. Changes to the format of PDB coordinate entry files will follow the Format Change Policy presented below and will be detailed in this Contents Guide. Beginning January 1997, the format of all PDB entries will be compliant with the current version of this Contents Guide.

Changes to the Contents Guide will be listed at the beginning in the What's New section and denoted by a fractional increase in the document version number. These changes may be of the following kind.

* Correction of typographical errors.
* Changes to the language for clarity.
* Addition or changes to the examples for better representation of format issues.
* Addition of new rules (these do not change the format but help to clarify the semantics).
* Addition of tokens to specification lists, such as in COMPND and SOURCE records, that are needed to more fully describe the structure and its biological source.
* Enhancements to the refinement and experimental details templates in the REMARK records. These remarks are currently being reviewed by several people in the community, and PDB expects to increase the level of detail archived, such as for NMR studies.
* Addition of new sections that enhance and expand the document (these may include topics such as PDB to mmCIF cross references or insertion of relevant sections from the PDB Deposition Form).

Format Change Policy

The PDB will use the following protocol in making changes to the way PDB coordinate entries are represented and archived. The purpose of the new policy is to allow ample time for everyone to understand these changes and to assess their impact on existing programs. These modifications are necessary to address the changing needs of our users as well as the changing nature of the data that is archived.

1. Comments and suggestions will be solicited from the community on specific problems and data representation issues as they arise.
2. Proposed format changes will be disseminated through the PDB Listserver (pdb-l@pdb.pdb.bnl.gov) and PDB's Internet sites (WWW, FTP, and Gopher). They will also be summarized in the PDB Quarterly Newsletter.
3. A sixty-day discussion period will follow the announcement of proposed changes. Comments and suggestions must be received within this time period. Major changes which are not upwardly compatible will be allotted up to twice the standard amount of discussion time.
4. This sixty-day discussion period will be followed by a thirty-day period in which the PDB staff, the PDB Advisory Board, and the User Group Chair will evaluate and reconcile all suggestions. The final decision pertaining to the format change, which lies with the Advisory Board Chair, will then be officially announced via the PDB Listserver and PDB's Internet sites (WWW, FTP, and Gopher).
5. Implementation will follow official announcement of the format change. Major changes will not appear in PDB files earlier than sixty days after the announcement, allowing sufficient time to modify files and programs.
6. Changes will be released no more than twice a year, unless extraordinary circumstances require action. This will be done only in consultation with the Advisory Board and following the usual ninety-day discussion and evaluation period.

The PDB format has been in use since the late 1970's. A number of groups including the mmCIF Committee have been looking at ways to upgrade both the file content and the interchange format used by PDB. This is clearly needed due to changes in the data that PDB archives, the size of the database itself, and finally, to allow PDB to use more up-to-date methods for representing and storing biological data.

The PDB plans to be prudent and deliberate in making changes to the current PDB files in order to minimize the need to change existing programs. In particular, we will explore ways and means of ensuring that programs which read the current ATOM/HETATM records can continue to do so in the foreseeable future.

The PDB wishes to acknowledge Dr. Gerald Selzer of the National Science Foundation who urged us to formulate this policy.

Basic Notions of the Format Description

Character Set

Only non-control ASCII characters, as well as the space and end-of-line indicator, appear in a PDB coordinate entry file. Namely:

abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ

1234567890

` - = [ ] \ ; ' , . / ~ ! @ # $ % ^ & * ( ) _ + { } | : " < > ?

the space, and end-of-line. The end-of-line indicator is system-specific. Unix uses a line feed character; other systems may use a carriage return followed by a line feed.

Special Characters

Greek letters are spelled out, i.e., alpha, beta, gamma, etc.

Bullets are represented as (DOT).

Right arrow is represented as -->.

Left arrow is represented as <--.

Superscripts are initiated and terminated by double equal signs, e.g., S==2+==.

Subscripts are initiated and terminated by single equal signs, e.g., F=c=.

If "=" is surrounded by at least one space on each side, then it is assumed to be an equal sign, e.g., 2 + 4 = 6.

Commas, colons, and semi-colons are used as list delimiters in records which have one of the following data types:

List
SList
Specification List
Specification

If a comma, colon, or semi-colon is used in any context other than as a delimiting character, then the character must be escaped, i.e., immediately preceded by a backslash, "\". Examples of this use are found in line 4 of each of the following:

COMPND    MOL_ID: 1;                                                       
COMPND   2 MOLECULE: GLUTATHIONE SYNTHETASE;                               
COMPND   3 CHAIN: NULL; 
COMPND   4 SYNONYM: GAMMA-L-GLUTAMYL-L-CYSTEINE\:GLYCINE LIGASE            
COMPND   5 (ADP-FORMING);                                                  
COMPND   6 EC: 6.3.2.3;                                                    
COMPND   7 ENGINEERED: YES                                                 
COMPND    MOL_ID: 1;                                                       
COMPND   2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHETASE;                      
COMPND   3 CHAIN: A, B;                                                    
COMPND   4 SYNONYM: MAT, ATP\:L-METHIONINE S-ADENOSYLTRANSFERASE;      
COMPND   5 EC: 2.5.1.6;                                                    
COMPND   6 ENGINEERED: YES;                                                
COMPND   7 BIOLOGICAL_UNIT: TETRAMER;                                      
COMPND   8 OTHER_DETAILS: TETRAGONAL MODIFICATION                          

Record Format

Every PDB file may be broken into a number of lines terminated by an end-of-line indicator. Each line in the PDB entry file consists of 80 columns. The last character in each PDB entry should be an end-of-line indicator.

Each line in the PDB file is self-identifying. The first six columns of every line contain a record name, left-justified and blank-filled. This must be an exact match to one of the stated record names.

The PDB file may also be viewed as a collection of record types. Each record type consists of one or more lines.

Each record type is further divided into fields.

Each record type is detailed in this document. The description of each record type includes the following sections:

* Overview
* Record Format
* Details
* Verification/Validation/Value Authority Control
* Relationship to Other Record Types
* Example
* Known Problems

For records that are fully described in fixed column format, columns not assigned to fields must be left blank.

Types of Records

It is possible to group records into categories based upon how often the record type appears in an entry.

Single

There are records which may only appear one time (without continuations) in a file. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                
------------------------------------------------------------------------------
CRYST1            Unit cell parameters, space group, and Z.                   
END               Last record in the file.                                    
HEADER            First line of the entry, contains PDB ID code,              
                  classification, and date of deposition.                     
MASTER            Control record for bookkeeping.                             
ORIGXn            Transformation from orthogonal coordinates to the submitted 
                  coordinates (n = 1, 2, or 3).                               
SCALEn            Transformation from orthogonal coordinates to fractional    
                  crystallographic coordinates (n = 1, 2, or 3).              

It is an error for a duplicate of any of these records to appear in an entry.

Single Continued

There are records that conceptually exist only once in an entry, but the information content may exceed the number of columns available. These records are therefore continued on subsequent lines. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                  
-------------------------------------------------------------------------------
AUTHOR            List of contributors.                                        
CAVEAT            Severe error indicator.  Entries with this record must be    
                  used with care.                                              
COMPND            Description of macromolecular contents of the entry.         
EXPDTA            Experimental technique used for the structure determination. 
KEYWDS            List of keywords describing the macromolecule.               
OBSLTE            Statement that the entry has been removed from distribution  
                  and list of the ID code(s) which replaced it.                
SOURCE            Biological source of macromolecules in the entry.          
SPRSDE            List of entries withdrawn from release and replaced by       
                  current entry.                                               
TITLE             Description of the experiment represented in the entry.      

The second and subsequent lines contain a continuation field which is a right-justified integer. This number increments by one for each additional line of the record, and is followed by a blank character.

Multiple

Most record types appear multiple times, often in groups where the information is not logically concatenated but is presented in the form of a list. Many of these record types have a custom serialization that may be used not only to order the records, but also to connect to other record types. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                   
--------------------------------------------------------------------------------
ANISOU            Anisotropic temperature factors.                              
ATOM              Atomic coordinate records for standard groups.                
CISPEP            Identification of peptide residues in cis conformation.       
CONECT            Connectivity records.                                         
DBREF             Reference to the entry in the sequence database(s).           
HELIX             Identification of helical substructures.                      
HET               Identification of non-standard groups or residues (heterogens)
HETSYN            Synonymous compound names for heterogens.                     
HYDBND            Identification of hydrogen bonds.                             
LINK              Identification of inter-residue bonds.                        
MODRES            Identification of modifications to standard residues.         
MTRIXn            Transformations expressing non-crystallographic symmetry      
                  (n = 1, 2, or 3). There may be multiple sets of these records.
REVDAT            Revision date and related information.                        
SEQADV            Identification of conflicts between PDB and the named sequence
                  database.                                                     
SEQRES            Primary sequence of backbone residues.                        
SHEET             Identification of sheet substructures.                        
SIGATM            Standard deviations of atomic parameters.                     
SIGUIJ            Standard deviations of anisotropic temperature factors.       
SITE              Identification of groups comprising important sites.          
SLTBRG            Identification of salt bridges                                
SSBOND            Identification of disulfide bonds.                            
TURN              Identification of turns.                                      
TVECT             Translation vector for infinite covalently connected          
                  structures.                                                   

Multiple Continued

There are records that conceptually exist multiple times in an entry, but the information content may exceed the number of columns available. These records are therefore continued on subsequent lines. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION
-------------------------------------------------------------------------------
FORMUL            Chemical formula of non-standard groups.                      
HETATM            Atomic coordinate records for heterogens.                     
HETNAM            Compound name of the heterogens.                              

The second and subsequent lines contain a continuation field which is a right-justified integer. This number increments by one for each additional line of the record, and is followed by a blank character.

Grouping

There are three record types used to group other records. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                  
-------------------------------------------------------------------------------
ENDMDL            End-of-model record for multiple structures in a single      
                  coordinate entry.                                            
MODEL             Specification of model number for multiple structures in a   
                  single coordinate entry.                                     
TER               Chain terminator.                                            

The MODEL/ENDMDL records surround groups of ATOM, HETATM, SIGATM, ANISOU, SIGUIJ, and TER records. TER records indicate the end of a chain.

Other

The remaining record types have a detailed inner structure. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                 
------------------------------------------------------------------------------
JRNL              Literature citation that defines the coordinate set.        
REMARK            General remarks, some are structured and some are free form.

Order of Records

All records in a PDB coordinate entry must appear in a defined order. Mandatory record types are present in all entries. When mandatory data are not provided, the record name must appear in the entry with a NULL indicator. Optional items become mandatory when certain conditions exist. Record order and existence are described in the following table:

RECORD TYPE             EXISTENCE      CONDITIONS IF OPTIONAL               
-------------------------------------------------------------------------------
HEADER                  Mandatory                                              
OBSLTE                  Optional       Mandatory in withdrawn entries.         
TITLE                   Mandatory                                              
CAVEAT                  Optional       Mandatory if structure is deemed        
                                       incorrect by an outside editorial board.
COMPND                  Mandatory                                              
SOURCE                  Mandatory                                              
KEYWDS                  Mandatory                                              
EXPDTA                  Mandatory                                              
AUTHOR                  Mandatory                                              
REVDAT                  Mandatory                                              
SPRSDE                  Optional       Mandatory if a replacement entry.      
JRNL                    Optional       Mandatory if a publication describes    
                                       the experiment.                         
REMARK 1                Optional                                               
REMARK 2                Mandatory                                              
REMARK 3                Mandatory                                              
REMARK N                Optional       Mandatory under certain conditions, as   
                                       noted in the remark descriptions.
DBREF                   Optional       Mandatory for each peptide chain with a 
                                       length greater than ten (10) residues, 
                                       and for nucleic acid entries that exist 
                                       in the Nucleic Acid Database (NDB).     
SEQADV                  Optional       Mandatory if sequence conflict exists.  
SEQRES                  Optional       Mandatory if ATOM records exist.      
MODRES                  Optional       Mandatory if modified group exists      
                                       within the coordinates.
HET                     Optional       Mandatory if non-standard group other  
                                       than water appears in the entry.       
HETNAM                  Optional       Mandatory if non-standard group other  
                                       than water appears in the entry.
HETSYN                  Optional                                     
FORMUL                  Optional       Mandatory if non-standard group or      
                                       water appears.                          
HELIX                   Optional                      
SHEET                   Optional                       
TURN                    Optional                         
SSBOND                  Optional       Mandatory if disulfide bond is present. 
LINK                    Optional                                               
HYDBND                  Optional                                               
SLTBRG                  Optional                                               
CISPEP                  Optional                                               
SITE                    Optional                                               
CRYST1                  Mandatory                                              
ORIGX1 ORIGX2 ORIGX3    Mandatory                                              
SCALE1 SCALE2 SCALE3    Mandatory                                              
MTRIX1 MTRIX2 MTRIX3    Optional       Mandatory if the complete asymmetric    
                                       unit must be generated from the given   
                                       coordinates using                       
                                       non-crystallographic symmetry.          
TVECT                   Optional                        
MODEL                   Optional       Mandatory if more than one model    
                                       is present in the entry.                
ATOM                    Optional       Mandatory if standard residues exist.   
SIGATM                  Optional                                               
ANISOU                  Optional                                               
SIGUIJ                  Optional                                               
TER                     Optional       Mandatory if ATOM records exist.        
HETATM                  Optional       Mandatory if non-standard group appears.
ENDMDL                  Optional       Mandatory if MODEL appears.             
CONECT                  Optional       Mandatory if non-standard group         
                                       appears.                                
MASTER                  Mandatory                                              
END                     Mandatory                                              

Note that a PDB file existing outside of the PDB official release may contain locally-defined records beginning with "USER". The PDB reserves the right to add new record types (not beginning with "USER"), so programs which read PDB entries should be prepared to read (and ignore) other record types. PDB will follow standard procedures whenever format changes are proposed.

Sections of an Entry

The following table lists the various sections of a PDB coordinate entry and the records comprising them:

SECTION              DESCRIPTION                    RECORD TYPE                 
--------------------------------------------------------------------------------
Title                Summary descriptive remarks    HEADER, OBSLTE, TITLE,      
                                                    CAVEAT, COMPND, SOURCE,     
                                                    KEYWDS, EXPDTA, AUTHOR,     
                                                    REVDAT, SPRSDE, JRNL   
Remark               Bibliography, refinement,      REMARKs 1, 2, 3 and others  
                     annotations                                          
Primary structure    Peptide and/or nucleotide      DBREF, SEQADV, SEQRES MODRES
                     sequence and the                                       
                     relationship between the PDB                            
                     sequence and that found in                              
                     the sequence database(s)                            
Heterogen            Description of non-standard    HET, HETNAM, HETSYN, FORMUL 
                     groups                                                  
Secondary structure  Description of secondary       HELIX, SHEET, TURN    
                     structure                                               
Connectivity         Chemical connectivity          SSBOND, LINK, HYDBND,  
annotation                                          SLTBRG, CISPEP    
Miscellaneous        Features within the            SITE                   
  features           macromolecule                                          
Crystallographic     Description of the             CRYST1                  
                     crystallographic cell                                  
Coordinate           Coordinate transformation      ORIGXn, SCALEn, 
                                                    MTRIXn, TVECT
transformation       operators                                             
Coordinate           Atomic coordinate data         MODEL, ATOM, SIGATM, ANISOU, 
                                                    SIGUIJ, TER, HETATM, ENDMDL  
Connectivity         Chemical connectivity          CONECT
Bookkeeping          Summary information,           MASTER, END    
                     end-of-file marker                                          

The above information on Order of Records is repeated as Appendix 7.

Field Formats

Each record type is presented in a table which contains the division of the records into fields by column number, defined data type, field name or a quoted string which must appear in the field, and field definition. Any column not specified must be left blank.

Each field contains an identified data type which can be validated by a program. These are:

DATA TYPE          DESCRIPTION                                                    
----------------------------------------------------------------------------------
AChar              An alphabetic character (A-Z, a-z).    
Atom               Atom name which follow the naming rules in Appendix 3.         
Character          Any non-control character in the ASCII character set or a 
                   space.                                                    
Continuation       A two-character field that is either blank (for the first   
                   record of a set) or contains a two digit number             
                   right-justified and blank-filled which counts continuation  
                   records starting with 2.  The continuation number must be 
                   followed by a blank.                                        
Date               A 9 character string in the form dd-mmm-yy where DD is the 
                   day of the month, zero-filled on the left (e.g., 04); MMM is
                   the common English 3-letter abbreviation of the month; and   
                   YY is a year in the 20th century.  This must represent a     
                   valid date.                                                 
IDcode             A PDB identification code which consists of 4 characters,    
                   the first of which is a digit in the range 0 - 9; the       
                   remaining 3 are alpha-numeric, and letters are upper case    
                   only.  Entries with a 0 as the first character do not       
                   contain coordinate data.                                   
Integer            Right-justified blank-filled integer value.              
Token              A sequence of non-space characters followed by a colon and a 
                   space.                                                     
List               A String that is composed of text separated with commas.  
LString            A literal string of characters.  All spacing is significant 
                   and must be preserved.                                     
LString(n)         An LString with exactly n characters.                          
Real(n,m)          Real (floating point) number in the FORTRAN format Fn.m.       
Record name        The name of the record: 6 characters, left-justified and       
                   blank-filled.                                                  
Residue name       One of the standard amino acid or nucleic acids, as listed     
                   below, or the non-standard group designation as defined in     
                   the HET dictionary.  Field is right-justified.                  
SList              A String that is composed of text separated with semi-colons.  
Specification      A String composed of a token and its associated value          
                   separated by a colon.                                         
Specification      A sequence of Specifications, separated by semi-colons.        
list                                                                            
String             A sequence of characters.  These characters may have           
                   arbitrary spacing, but should be interpreted as directed       
                   below.                                                         
String(n)          A String with exactly n characters.                            
SymOP              An integer field of from 4 to 6 digits, right-justified, of   
                   the form nnnMMM where nnn is the symmetry operator number and  
                   MMM is the translation vector.  See details in Appendix 1.

To interpret a String, concatenate the contents of all continued fields together, collapse all sequences of multiple blanks to a single blank, and remove any leading and trailing blanks. This permits very long strings to be properly reconstructed.

The above information about field formats is repeated as Appendix 6.

Residue Names

Standard residue names used in PDB entries:

RESIDUE TYPE       RESIDUE NAME                                                   
----------------------------------------------------------------------------------
Amino acids        ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS,    
                   MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX               
Nucleic acids      A, C, G, T, U, I, +A, +C, +G, +T, +U, +I                       
Other              UNK (unknown)                                                  

See Appendix 4 for more information on the standard residue names and abbreviations, and Appendix 5 for their chemical formulas and molecular weights.


2. Title Section

This section contains records used to describe the experiment and the biological macromolecules present in the entry: HEADER, OBSLTE, TITLE, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRNL, and REMARK records.


HEADER

Overview

The HEADER record uniquely identifies a PDB entry through the idCode field. This record also provides a classification for the entry. Finally, it contains the date the coordinates were deposited at the PDB.

Record Format

COLUMNS        DATA TYPE       FIELD           DEFINITION                           
----------------------------------------------------------------------------------
 1 -  6        Record name     "HEADER"                                             
11 - 50        String(40)      classification  Classifies the molecule(s)           
51 - 59        Date            depDate         Deposition date.  This is the date   
                                               the coordinates were received by     
                                               the PDB                              
63 - 66        IDcode          idCode          This identifier is unique within PDB 

Details

* The classification string is left-justified and exactly matches one of a collection of strings. See the class list available from the WWW site. In the case of macromolecular complexes, the classification field must present a class for each macromolecule present. Due to the limited length of the classification field, strings must sometimes be abbreviated. In these cases, the full terms are given in KEYWDS.

* Classification may be based on function, metabolic role, molecule type, cellular location, etc. In the case of a molecule having a dual function, both may be presented here.

Verification/Validation/Value Authority Control

The verification program checks that the deposition date is a legitimate date and that the ID code is well-formed. PDB coordinate entry ID codes do not begin with 0, as this is used to identify the NOC files which are bibliographic only, not structural entries. The status and deposition date of an entry are checked against the PDB SYBASE tables, which provide a definitive list of existing ID codes.

Relationships to Other Record Types

The classification found in HEADER also appears in KEYWDS, unabbreviated and in no strict order.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
HEADER    MUSCLE PROTEIN                          02-JUN-93   1MYS
HEADER    HYDROLASE (CARBOXYLIC ESTER)            08-APR-93   2PHI
HEADER    COMPLEX (LECTIN/TRANSFERRIN)            07-JAN-94   1LGB


OBSLTE

Overview

OBSLTE appears in entries which have been withdrawn from distribution.

This record acts as a flag in an entry which has been withdrawn from the PDB's full release. It indicates which, if any, new entries have replaced the withdrawn entry.

The format allows for the case of multiple new entries replacing one existing entry.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                          
----------------------------------------------------------------------------------
 1 -  6        Record name     "OBSLTE"                                           
 9 - 10        Continuation    continuation   Allows concatenation of multiple    
                                              records.                         
12 - 20        Date            repDate        Date that this entry was replaced.  
22 - 25        IDcode          idCode         ID code of this entry.              
32 - 35        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           
37 - 40        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           
42 - 45        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           
47 - 50        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           
52 - 55        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           
57 - 60        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           
62 - 65        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           
67 - 70        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

Details

* It is PDB policy that only the primary author who submitted an entry has the authority to withdraw it. All withdrawn entries are available for research purposes. PDB should be contacted in cases where the withdrawn data are desired.

Verification/Validation/Value Authority Control

PDB staff add this record at the time an entry is removed from release.

Relationships to Other Record Types

None.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
OBSLTE     31-JAN-94 1MBP      2MBP


TITLE

Overview

The TITLE record contains a title for the experiment or analysis that is represented in the entry. It should identify an entry in the PDB in the same way that a title identifies a paper.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                            
----------------------------------------------------------------------------------
 1 -  6        Record name     "TITLE "                                             
 9 - 10        Continuation    continuation   Allows concatenation of multiple      
                                              records.                              
11 - 70        String          title          Title of the experiment.              

Details

* The title of the entry is free text and should describe the contents of the entry and any procedures or conditions that distinguish this entry from similar entries. It presents an opportunity for the depositor to emphasize the underlying purpose of this particular experiment.

* Some items that may be included in TITLE are:

- Experiment type.
- Description of the mutation.
- The fact that only alpha carbon coordinates have been provided in the entry.

Verification/Validation/Value Authority Control

This record is free text so no verification of format is required. The title is supplied by the depositor, but PDB staff may exercise editorial judgment in consultation with depositors in assigning the title.

Relationships to Other Record Types

COMPND, SOURCE, EXPDTA, and REMARKs provide information that may also be found in TITLE. You may think of the title as describing the experiment, and the compound record as describing the molecule(s).

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
TITLE     RHIZOPUSPEPSIN COMPLEXED WITH REDUCED PEPTIDE INHIBITOR
TITLE     BETA-GLUCOSYLTRANSFERASE, ALPHA CARBON COORDINATES ONLY
TITLE     NMR STUDY OF OXIDIZED THIOREDOXIN MUTANT (C62A,C69A,C73A)
TITLE    2 MINIMIZED AVERAGE STRUCTURE


CAVEAT

Overview

CAVEAT warns of severe errors in an entry. Use caution when using an entry containing this record.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                          
----------------------------------------------------------------------------------
 1 -  6        Record name     "CAVEAT"                                           
 9 - 10        Continuation    continuation   Allows concatenation of multiple    
                                              records.                            
12 - 15        IDcode          idCode         PDB ID code of this entry.          
20 - 70        String          comment        Free text giving the reason for the 
                                              CAVEAT.                             

Details

* PDB will add this record to incorrect entries that are not withdrawn from the set of released entries. This record will be used sparingly, and only after an external review has been made.

* Please note the CAVEAT will also be included in cases where PDB is unable to verify the transformation back to the crystallographic cell. In these cases, the molecular structure may still be correct.

Verification/Validation/Value Authority Control

CAVEAT will be added by the PDB to entries known to be incorrect.

Relationships to Other Record Types

REMARK 5 repeats the comment field of the CAVEAT record.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
CAVEAT     1ABC    THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS
CAVEAT   2 1ABC    UNCORRECTABLE AT THIS TIME


COMPND

Overview

The COMPND record describes the macromolecular contents of an entry. Each macromolecule found in the entry is described by a set of token: value pairs, and is referred to as a COMPND record component. Since the concept of a molecule is difficult to specify exactly, PDB staff may exercise editorial judgment in consultation with depositors in assigning these names.

For each macromolecular component, the molecule name, synonyms, number assigned by the Enzyme Commission (EC), and other relevant details are specified.

Record Format

COLUMNS        DATA TYPE         FIELD          DEFINITION                        
----------------------------------------------------------------------------------
 1 -  6        Record name       "COMPND"                                         
 9 - 10        Continuation      continuation   Allows concatenation of multiple  
                                                records.                          
11 - 70        Specification     compound       Description of the molecular      
               list                             components.                  

Details

* The compound record is a Specification list. The specifications, or tokens, that may be used are listed below:

TOKEN                   VALUE DEFINITION                                       
---------------------------------------------------------------------------------
MOL_ID                  Numbers each component; also used in SOURCE to associate 
                        the information.   
MOLECULE                Name of the macromolecule.         
CHAIN                   Comma-separated list of chain identifier(s). "NULL" is   
                        used to indicate a blank chain identifier.     
FRAGMENT                Specifies a domain or region of the molecule.            
SYNONYM                 Comma-separated list of synonyms for the MOLECULE.       
EC                      The Enzyme Commission number associated with the         
                        molecule. If there is more than one EC number, they     
                        are presented as a comma-separated list.                 
ENGINEERED              Indicates that the molecule was produced using           
                        recombinant technology or by purely chemical synthesis.  
MUTATION                Describes mutations from the wild type molecule.         
BIOLOGICAL_UNIT         If the MOLECULE functions as part of a larger            
                        biological unit, the entire functional unit may be       
                        described.                                               
OTHER_DETAILS           Additional comments.                                     

* In the general case the PDB tends to reflect the biological/functional view of the molecule. For example, the hetero-tetramer hemoglobin molecule is treated as a discrete component in COMPND.

* In the case of synthetic molecules, e. g., hybrids, the description will be provided by the depositor.

* No specific rules apply to the ordering of the tokens, except that the occurrence of MOL_ID or FRAGMENT indicates that the subsequent tokens are related to that specific molecule or fragment of the molecule.

* Physical layout of these items may be altered by PDB staff to improve human readability of the COMPND record.

* Asterisks in nucleic acid names (in MOLECULE) are for ease of reading.

* When insertion codes are given as part of the residue name, they must be given within square brackets, i.e., H57[A]N. This might occur when listing residues in FRAGMENT, MUTATION, or OTHER_DETAILS.

* For multi-chain molecules, e.g., the hemoglobin tetramer, a comma-separated list of CHAIN identifiers is used.

* When non-blank chain identifiers occur in the entry, they must be specified.

* NULL is used to indicate blank chain identifiers. E.g., CHAIN: NULL, CHAIN: NULL, B, C.

* For enzymes, if no EC number has been assigned, "EC: NOT ASSIGNED" is used.

* ENGINEERED is followed either by "YES" or by a comment.

* For the token MUTATION, the following set of examples illustrate the conventions used by PDB to represent various types of mutations.

   MUTATION TYPE         DESCRIPTION                     FORM   
   ------------------------------------------------------------------------------
   Simple substitution   His 57 replaced by Asn          H57N 
                         His 57A replaced by Asn, in       
                         chain C only                    Chain C, H57[A]N
   Insertion             His and Pro inserted before      
                         Lys 48                          INS(HP-K48) 
   Deletion              Arg 141 of chains A and C        
                         deleted, not deleted in           
                         chain B                         Chain A, C, DEL(R141)
                         His 23 through ARG 26 deleted   DEL(23-26)
                         His 23C and Arg 26 deleted       
                         from chain B only               Chain B, DEL(H23[C],R26)

* When there are more than ten mutations:

- All the mutations are listed in the SEQADV record.
- Some mutations may be listed in MUTATION in COMPND to highlight the most important ones, at the depositor's discretion.

* New tokens may be added by the PDB as needed.

Verification/Validation/Value Authority Control

CHAIN must match the chain identifiers(s) of the molecule(s). EC numbers are checked against the Enzyme Data Bank.

Relationships to Other Record Types

Each molecule given a MOL_ID in COMPND must be listed and given the biological source information in SOURCE. In the case of mutations, the SEQADV records will present differences from the reference molecule. REMARK record may further describe the contents of the entry. Also see verification above.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
COMPND    MOL_ID: 1;                                                  
COMPND   2 MOLECULE: HEMOGLOBIN;                                      
COMPND   3 CHAIN: A, B, C, D;                                         
COMPND   4 ENGINEERED: YES;                                           
COMPND   5 MUTATION: CHAIN B, D, V1A;                                 
COMPND   6 BIOLOGICAL_UNIT: HEMOGLOBIN EXISTS AS AN A1B1/A2B2         
COMPND   7 TETRAMER;
COMPND   8 OTHER_DETAILS: DEOXY FORM  
COMPND    MOL_ID: 1;                                            
COMPND   2 MOLECULE: COWPEA CHLOROTIC MOTTLE VIRUS;             
COMPND   3 CHAIN: A, B, C;                                      
COMPND   4 SYNONYM: CCMV;                                       
COMPND   5 MOL_ID: 2;                                           
COMPND   6 MOLECULE: RNA (5'-(*AP*UP*AP*U)-3');               
COMPND   7 CHAIN: D, F;
COMPND   8 ENGINEERED: YES;                                     
COMPND   9 MOL_ID: 3;                                           
COMPND  10 MOLECULE: RNA (5'-(*AP*U)-3');                      
COMPND  11 CHAIN: E;
COMPND  12 ENGINEERED: YES
COMPND    MOL_ID: 1;                                            
COMPND   2 MOLECULE: HEVAMINE A;                                
COMPND   3 CHAIN: NULL;                                         
COMPND   4 EC: 3.2.1.14, 3.2.1.17;                              
COMPND   5 OTHER_DETAILS: PLANT ENDOCHITINASE/LYSOZYME          


SOURCE

Overview

The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied.

Record Format

COLUMNS        DATA TYPE         FIELD          DEFINITION                        
----------------------------------------------------------------------------------
 1 -  6        Record name       "SOURCE"                                         
 9 - 10        Continuation      continuation   Allows concatenation of multiple  
                                                records.                         
11 - 70        Specification     srcName        Identifies the source of the      
               list                             macromolecule in a token: value 
                                                format.                        

Details

TOKEN                                VALUE DEFINITION                        
---------------------------------------------------------------------------------
MOL_ID                               Numbers each molecule.  Same as appears in  
                                     COMPND.                                     
SYNTHETIC                            Indicates a chemically-synthesized source.  
FRAGMENT                             A domain or fragment of the molecule may be 
                                     specified.                                  
ORGANISM_SCIENTIFIC                  Scientific name of the organism.            
ORGANISM_COMMON                      Common name of the organism.                
STRAIN                               Identifies the strain.                      
VARIANT                              Identifies the variant.                     
CELL_LINE                            The specific line of cells used in the      
                                     experiment.                                 
ATCC                                 American Type Culture Collection tissue     
                                     culture number.                             
ORGAN                                Organized group of tissues that carries on  
                                     a specialized function.                     
TISSUE                               Organized group of cells with a common     
                                     function and structure.                     
CELL                                 Identifies the particular cell type.        
ORGANELLE                            Organized structure within a cell.          
SECRETION                            Identifies the secretion, such as saliva, 
                                     urine, or venom, from which the molecule was
                                     isolated. 
CELLULAR_LOCATION                    Identifies the location inside (or
                                     outside) the cell.
PLASMID                              Identifies the plasmid containing the gene. 
GENE                                 Identifies the gene.                        
EXPRESSION_SYSTEM                    System used to express recombinant         
                                     macromolecules.                             
EXPRESSION_SYSTEM_STRAIN             Strain of the organism in which the molecule
                                     was expressed.                              
EXPRESSION_SYSTEM_VARIANT            Variant of the organism used as the 
                                     expression system.
EXPRESSION_SYSTEM_CELL_LINE          The specific line of cells used as the 
                                     expression system.
EXPRESSION_SYSTEM_ATCC_NUMBER        Identifies the ATCC number of the expression
                                     system
EXPRESSION_SYSTEM_ORGAN              Specific organ which expressed the molecule.
EXPRESSION_SYSTEM_TISSUE             Specific tissue which expressed the molecule.
EXPRESSION_SYSTEM_CELL               Specific cell type which expressed the 
                                     molecule.
EXPRESSION_SYSTEM_ORGANELLE          Specific organelle which expressed the 
                                     molecule.
EXPRESSION_SYSTEM_CELLULAR_LOCATION  Identifies the location inside or outside 
                                     the cell which expressed the molecule.
EXPRESSION_SYSTEM_VECTOR_TYPE        Identifies the type of vector used, i.e., 
                                     plasmid, virus, or cosmid.
EXPRESSION_SYSTEM_VECTOR             Identifies the vector used.
EXPRESSION_SYSTEM_PLASMID            Plasmid used in the recombinant experiment. 
EXPRESSION_SYSTEM_GENE               Name of the gene used in recombinant       
                                     experiment.                                
OTHER_DETAILS                        Used to present information on the source 
                                     which is not given elsewhere.              

* The srcName is a list of token: value pairs describing each biological component of the entry.

* As in COMPND, the order is not specified except that MOL_ID or FRAGMENT indicates subsequent specifications are related to that molecule or fragment of the molecule.

* Physical layout of these items may be altered by PDB staff to improve human readability of the SOURCE record.

* Only the relevant tokens need to appear in an entry.

* Molecules prepared by purely chemical synthetic methods are described by the specification SYNTHETIC followed by "YES" or an optional value, such as NON-BIOLOGICAL SOURCE or BASED ON THE NATURAL SEQUENCE. ENGINEERED must appear in the COMPND record.

* In the case of a chemically synthesized molecule using a biologically functional sequence (nucleic or amino acid), SOURCE reflects the biological origin of the sequence and COMPND reflects its synthetic nature by inclusion of the token ENGINEERED. The token SYNTHETIC appears in SOURCE.

* If made from a synthetic gene, ENGINEERED appears in COMPND and the expression system is described in SOURCE (SYNTHETIC does NOT appear in SOURCE).

* If the molecule was made using recombinant techniques, ENGINEERED appears in COMPND and the system is described in SOURCE.

* When multiple macromolecules appear in the entry, each MOL_ID, as given in the COMPND record, must be repeated in the SOURCE record along with the source information for the corresponding molecule.

* Hybrid molecules prepared by fusion of genes are treated as multi-molecular systems for the purpose of specifying the source. The token FRAGMENT is used to associate the source with its corresponding fragment.

- When necessary to fully describe hybrid molecules, tokens may appear more than once for a given MOL_ID.
- All relevant token: value pairs that taken together fully describe each fragment are grouped following the appropriate FRAGMENT.
- Descriptors relative to the full system appear before the FRAGMENT (see Example 3 below).

* ORGANISM_SCIENTIFIC provides the Latin genus and species. Virus names are listed as the scientific name.

* Cellular origin is described by giving cellular compartment, organelle, cell, tissue, organ, or body part from which the molecule was isolated.

* CELLULAR_LOCATION may be used to indicate where in the organism the compound was found. Examples are: extracellular, periplasmic, cytosol.

* Entries containing molecules prepared by recombinant techniques are described as follows:

- The expression system is described.
- The organism and cell location given are for the source of the gene used in the cloning experiment.
- Transgenic organisms, such as mouse producing human proteins, are treated as expression systems.

* For a theoretical modelling experiment, SOURCE describes the modelled compound just as though it were an experimental study.

* New tokens may be added by the PDB.

Verification/Validation/Value Authority Control

The biological source is compared to that found in the sequence database. Common and scientific names are checked against the "Annotated Classification of Source Organisms: PIR-International Protein Sequence Database" compiled by Andrzej Elzanowski and available from the PDB.

Relationships to Other Record Types

Each macromolecule listed in COMPND must have a corresponding source.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SOURCE    MOL_ID: 1;                                   
SOURCE   2 ORGANISM_SCIENTIFIC: AVIAN SARCOMA VIRUS;   
SOURCE   3 STRAIN: SCHMIDT-RUPPIN B;                   
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;        
SOURCE   5 EXPRESSION_SYSTEM_PLASMID: PRC23IN
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
SOURCE   3 ORGANISM_COMMON: CHICKEN;
SOURCE   4 ORGAN: HEART;
SOURCE   5 TISSUE: MUSCLE
SOURCE    MOL_ID: 1;
SOURCE   2 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   3 EXPRESSION_SYSTEM_STRAIN: BE167;
SOURCE   4 FRAGMENT: RESIDUES 1-16;
SOURCE   5 ORGANISM_SCIENTIFIC: BACILLUS AMYLOLIQUEFACIENS;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 FRAGMENT: RESIDUES 17-214;
SOURCE   8 ORGANISM_SCIENTIFIC: BACILLUS MACERANS


KEYWDS

Overview

The KEYWDS record contains a set of terms relevant to the entry. Terms in the KEYWDS record provide a simple means of categorizing entries and may be used to generate index files. This record addresses some of the limitations found in the classification field of the HEADER record. It provides the opportunity to add further annotation to the entry in a concise and computer-searchable fashion.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
---------------------------------------------------------------------------------
 1 -  6        Record name     "KEYWDS"                                          
 9 - 10        Continuation    continuation   Allows concatenation of records if 
                                              necessary.                         
11 - 70        List            keywds         Comma-separated list of keywords   
                                              relevant to the entry.            

Details

* The KEYWDS record contains a list of terms relevant to the entry, similar to that found in journal articles. A phrase may be used if it presents a single concept (e.g., reaction center). Terms provided in this record may include those that describe the following:

- Functional classification.
- Metabolic role.
- Known biological or chemical activity.
- Structural classification.

*Other classifying terms may be used. No ordering is required for these terms. A number of PDB entries contain complexes of macromolecules. In these cases, all terms applicable to each molecule should be provided.

*Note that the terms in the KEYWDS record duplicate those found in the classification field of the HEADER record. Terms abbreviated in the HEADER record are unabbreviated in KEYWDS, and the parentheses used in HEADER are optional in KEYWDS.

Verification/Validation/Value Authority Control

Terms used in the KEYWDS record are subject to scientific and editorial review. A list of terms, definitions, and synonyms will be maintained at the PDB. Every attempt will be made to provide some level of consistency with keywords used in other biological databases.

Relationships to Other Record Types

HEADER records contain a classification term which must also appear in KEYWDS. Scientific judgment will dictate when terms used in one entry to describe a molecule should be included in other entries with the same or similar molecules.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
KEYWDS    LYASE, TRICARBOXYLIC ACID CYCLE, MITOCHONDRION, OXIDATIVE
KEYWDS   2 METABOLISM


EXPDTA

Overview

The EXPDTA record presents information about the experiment.

The EXPDTA record identifies the experimental technique used. This may refer to the type of radiation and sample, or include the spectroscopic or modeling technique. Permitted values include:

ELECTRON DIFFRACTION
FIBER DIFFRACTION
FLUORESCENCE TRANSFER
NEUTRON DIFFRACTION
NMR
THEORETICAL MODEL
X-RAY DIFFRACTION

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                          
-------------------------------------------------------------------------------
 1 -  6       Record name    "EXPDTA"                                          
 9 - 10       Continuation   continuation  Allows concatenation of multiple    
                                           records.                            
11 - 70       SList          technique     The experimental technique(s) with  
                                           optional comment describing the     
                                           sample or experiment. 

Details

* EXPDTA is mandatory and appears in all entries.

* The technique must match one of the permitted values. See above.

* If more than one model appears in the entry, the number of models included must be stated.

* If only one model appears in the entry, its significance must be stated, such as it being a minimized average or regularized mean structure.

* If more than one technique was used for the structure determination and is being represented in the entry, EXPDTA presents the techniques as a semi-colon separated list. Each technique may have a comment, which appears before the semi-colon.

Verification/Validation/Value Authority Control

The verification program checks that the EXPDTA record appears in the entry and that the technique matches one of the allowed values. It also checks that the relevant standard REMARK is added in the case of NMR, fiber, or theoretical modeling studies, and that the correct CRYST1 and SCALE are used in these cases. If an entry contains multiple models, the verification program checks for the correct number of matching MODEL/ENDMDL records.

Relationships to Other Record Types

If the experiment is an NMR, fiber, or theoretical modeling study, this may be stated in the TITLE, and the appropriate EXPDTA and REMARK records should appear. Specific details of the data collection and experiment appear in the REMARKs.

In the case of a polycrystalline fiber diffraction study, CRYST1 and SCALE contain the normal unit cell data.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
EXPDTA    X-RAY DIFFRACTION
EXPDTA    NEUTRON DIFFRACTION; X-RAY DIFFRACTION
EXPDTA    NMR, 32 STRUCTURES
EXPDTA    NMR, REGULARIZED MEAN STRUCTURE
EXPDTA    THEORETICAL MODEL
EXPDTA    FIBER DIFFRACTION, FIBER
EXPDTA    FIBER DIFFRACTION, POLYCRYSTALLINE SAMPLE


AUTHOR

Overview

The AUTHOR record contains the names of the people responsible for the contents of the entry.

Record Format

 
COLUMNS       DATA TYPE      FIELD         DEFINITION                             
----------------------------------------------------------------------------------
 1 -  6       Record name    "AUTHOR"                                             
 9 - 10       Continuation   continuation  Allows concatenation of multiple       
                                           records.                               
11 - 70       List           authorList    List of the author names, separated    
                                           by commas.                             

Details

* The authorList field lists author names separated by commas with no subsequent spaces.

* Representation of personal names:

- First and middle names are indicated by initials, each followed by a period, and precede the surname.
- Only the surname (family or last name) of the author is given in full.
- Hyphens can be used if they are part of the author's name.
- Apostrophes are allowed in surnames.
- The word Junior is not abbreviated.
- Umlauts and other character modifiers are not given.

* Structure of personal names:

- There is no space after any initial and its following period.
- Blank spaces are used in a name only if properly part of the surname (e.g., J.VAN DORN), or between surname and Junior, II, or III.
- Abbreviations that are part of a surname, such as St. or Ste., are followed by a period and a space before the next part of the surname.

* Representation of corporate names:

- Group names used for one or all of the authors should be spelled out in full.
- The name of the larger group comes before the name of a subdivision, e.g., University of Somewhere Department of Chemistry.

* Structure of list:

- Line breaks between multiple lines in the authorList occur only after a comma.
- Personal names are not split across two lines.

* Special cases:

- Names are given in English if there is an accepted English version; otherwise in the native language, transliterated if necessary.
- "ET AL." may be used when all authors are not individually listed.

Verification/Validation/Value Authority Control

The verification program checks that the authorList field is correctly formatted. It does not perform any spelling checks or name verification.

Relationships to Other Record Types

The format of the names in the AUTHOR record is the same as in JRNL and REMARK 1 references.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
AUTHOR    M.B.BERRY,B.MEADOR,T.BILDERBACK,P.LIANG,M.GLASER,
AUTHOR   2 G.N.PHILLIPS JUNIOR,T.L.ST. STEVENS
AUTHOR    C.-I.BRANDEN,C.J.BIRKETT-CLEWS,L.RIVA DI SANSAVERINO


REVDAT

Overview

REVDAT records contain a history of the modifications made to an entry since its release.

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                             
----------------------------------------------------------------------------------
 1 -  6       Record name    "REVDAT"                                             
 8 - 10       Integer        modNum        Modification number.                   
11 - 12       Continuation   continuation  Allows concatenation of multiple      
                                           records.                         
14 - 22       Date           modDate       Date of modification (or release for   
                                           new entries).  This is not repeated    
                                           on continuation lines.                 
24 - 28       String(5)      modId         Identifies this particular             
                                           modification.  It links to the         
                                           archive used internally by PDB.        
                                           This is not repeated on continuation   
                                           lines.                                 
32            Integer        modType       An integer identifying the type of     
                                           modification.  In case of revisions    
                                           with more than one possible modType,   
                                           the highest value applicable will be   
                                           assigned.                              
40 - 45       LString(6)     record        Name of the modified record.           
47 - 52       LString(6)     record        Name of the modified record.           
54 - 59       LString(6)     record        Name of the modified record.           
61 - 66       LString(6)     record        Name of the modified record.           

Details

* Each time revisions are made to the entry, a modification number is assigned in increasing (by 1) numerical order. REVDAT records appear in descending order (most recent modification appears first). New entries have a REVDAT record with modNum equal to 1 and modType equal to 0. Allowed modTypes are:

         0       Initial released entry. 
         1       Miscellaneous - mostly typographical.   
         2       Modification of a CONECT record.        
         3       Modification to coordinates or transformations. 
         4 - 9   Not defined.

* Each revision may have more than one REVDAT record, and each revision has a separate continuation field.

Verification/Validation/Value Authority Control

The modType must be one of the defined types, and the given record type must be valid. If modType is 0, the modId must match the entry's ID code in the HEADER record.

Relationships to Other Record Types

REMARK 860 presents the correction or change that is made to an entry. Also, see verification above.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REVDAT   3   15-OCT-89 1PRCB   1       REMARK                         
REVDAT   2   19-APR-89 1PRCA   2       CONECT                         
REVDAT   1   09-JAN-89 1PRC    0                                      


SPRSDE

Overview

The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set. One entry may replace many. It is PDB policy that only the principal investigator of a structure has the authority to withdraw it.

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                             
----------------------------------------------------------------------------------
 1 -  6       Record name    "SPRSDE"                                             
 9 - 10       Continuation   continuation  Allows for multiple ID codes.          
12 - 20       Date           sprsdeDate    Date this entry superseded the         
                                           listed entries. This field is not      
                                           copied on continuations.               
22 - 25       IDcode         idCode        ID code of this entry.  This field     
                                           is not copied on continuations.        
32 - 35       IDcode         sIdCode       ID code of a superseded entry.         
37 - 40       IDcode         sIdCode       ID code of a superseded entry.         
42 - 45       IDcode         sIdCode       ID code of a superseded entry.         
47 - 50       IDcode         sIdCode       ID code of a superseded entry.         
52 - 55       IDcode         sIdCode       ID code of a superseded entry.         
57 - 60       IDcode         sIdCode       ID code of a superseded entry.         
62 - 65       IDcode         sIdCode       ID code of a superseded entry.         
67 - 70       IDcode         sIdCode       ID code of a superseded entry.         

Details

* The ID code list is terminated by the first blank sIDcode field.

Verification/Validation/Value Authority Control

PDB checks that the superseded entries have actually been withdrawn from release.

Relationships to Other Record Types

The sprsdeDate is usually the date the entry is released, and therefore matches the date in the REVDAT 1 record. The ID code found in the idCode field must be the same as one found in the idCode field of the HEADER record.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SPRSDE     17-JUL-84 4HHB      1HHB
SPRSDE     27-FEB-95 1GDJ      1LH4 2LH4


JRNL

Overview

The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set. There is at most one JRNL reference per entry. If there is no primary reference, then there is no JRNL reference. Other references are given in REMARK 1.

PDB is in the process of linking and/or adding all references to CitDB, the literature database used by the Genome Data Base (available at URL http://gdbwww.gdb.org/gdb-bin/genera/genera/citation/Citation).

Record Format

COLUMNS    DATA TYPE      FIELD     DEFINITION                                   
----------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                               
13 - 70    LString        text      See Details below.                            

Details

* The following tables are used to describe the sub-record types of the JRNL record.

* The AUTH sub-record is mandatory in JRNL. This is followed by TITL, EDIT, REF, PUBL, and REFN sub-record types. REF and REFN are also mandatory in JRNL. EDIT and PUBL may appear only if the reference is to a non-journal.

* If the JRNL reference is in the MEDLINE database the information in the MEDLINE reference will be used to supply information for the sub-record types.

* When a MEDLINE reference is used, the abbreviation of the journal will be converted to the CASSI abbreviation as listed in the coden list used jointly by the Cambridge Crystallographic Data Centre (CCDC) and the PDB.

1. AUTH

* AUTH contains the list of authors associated with the cited article or contribution to a larger work (i.e., AUTH is not used for the editor of a book).

* The author list is formatted similarly to the AUTHOR record. It is a comma-separated list of names. Spaces at the end of a sub-record are not significant; all other spaces are significant. See the AUTHOR record for full details.

* The authorList field of continuation sub-records in JRNL differs from that in AUTHOR by leaving no leading blank in column 20 of any continuation lines.

* One author's name, consisting of the initials and family name, cannot be split across two lines. If there are continuation sub-records, then all but the last sub-record must end in a comma.

COLUMNS    DATA TYPE      FIELD         DEFINITION                               
-------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                               
13 - 16    LString(4)     "AUTH"        Appears on all continuation records.     
17 - 18    Continuation   continuation  Allows concatenation of multiple         
                                        records.                                 
20 - 70    List           authorList    List of the authors.                     

2. TITL

* TITL specifies the title of the reference. This is used for the title of a journal article, chapter, or part of a book. The TITL line is omitted if the author(s) listed in authorList wrote the entire book (or other work) listed in REF and no section of the book is being cited.

* If an article is in a language other than English and is printed with an alternate title in English, the English language title is given, followed by a space and then the name of the language (in its English form, in square brackets) in which the article is written.

* If the title of an article is in a non-Roman alphabet the title is transliterated.

* The actual title cited is reconstructed in a manner identical to other continued records, i.e., trailing blanks are discarded and the continuation line is concatenated with a space inserted.

* A line cannot end with a hyphen. A compound term (two elements connected by a hyphen) or chemical names which include a hyphen must appear on a single line, unless they are too long to fit on one line, in which case the split is made at a normally-occurring hyphen. An individual word cannot be hyphenated at the end of a line and put on two lines. An exception is when there is a repeating compound term where the second element is omitted, e.g., "DOUBLE- AND TRIPLE-RESONANCE". In such a case the non-completed word "DOUBLE-" could end a line and not alter reconstruction of the title.

COLUMNS    DATA TYPE      FIELD         DEFINITION                               
-------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                               
13 - 16    LString(4)     "TITL"        Appears on all continuation lines.        
17 - 18    Continuation   continuation  Permits long titles.                      
20 - 70    LString        title         Title of the article.                     

3. EDIT

* EDIT appears if editors are associated with a non-journal reference. The editor list is formatted and concatenated in the same way that author lists are.

COLUMNS    DATA TYPE      FIELD         DEFINITION                               
-------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                               
13 - 16    LString(4)     "EDIT"        Appears on all continuation records.      
17 - 18    Continuation   continuation  Allows a long list of editors.            
20 - 70    List           editorList    List of the editors.                      

4. REF

* REF is a group of fields which contains either the publication status or the name of the publication (and any supplement and/or report information), volume, page, and year. There are two forms of this sub-record group, depending upon the citation's publication status.

4a. If the reference has not yet been published, the sub-record type group has the form:

COLUMNS    DATA TYPE      FIELD                   DEFINITION                      
--------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                                
13 - 16    LString(3)     "REF"                                                   
20 - 34    LString(15)    "TO BE PUBLISHED"                                       

* At the present time, there is no formal mechanism in place for monitoring the subsequent publication of such referenced papers. PDB relies upon the depositor to provide reference update information since preliminary information can change by the time of actual publication.

4b. If the reference has been published, then the REF sub-record type contains information about the name of the publication, supplement, report, volume, page, and year in the appropriate fields. These fields are detailed below.

* Publication name (first item in pubName field):

- If the publication is a serial (i.e., a journal, an annual, or other non-book or non-monographic item issued in parts and intended to be continued indefinitely), use the abbreviated name of the publication as listed in American Chemical Society (A.C.S.) publications such as CAS Source Index (CASSI) or Chemical Abstracts. (The A.C.S. abbreviation is based on the International Standards Organization's standard ISO 4-1984[E].) If the A.C.S. has not yet established an abbreviation for the publication, the name is given in full.
- If the publication is a book, monograph, or other non-serial item, use its full name according to the Anglo-American Cataloging Rules, 2nd Ed., 1988 revision (AACR2R). (Non-serial items include theses, videos, computer programs, and anything that is complete in one or a finite number of parts.) If there is a sub-title, and the item is verified in an online catalog, it will be included using the same punctuation as in the source of verification. Preference will be given to verification using cataloging of the Library of Congress, the National Library of Medicine, and the British Library, in that order.
- If a book is part of a monographic series: the full name of the book (according to AACR2R) is listed first, followed by the name of the series in which it was published. The series information is given within parentheses and the series name is preceded by "IN:" and a space. If the series has an A.C.S. abbreviation, that abbreviation should be used; otherwise the series name should be listed in full. If applicable, the series name should be followed, after a comma and a space, by a volume (V.) and/or number (NO.) and/or part (PT.) indicator and the relevant characters to indicate its number and/or letter in the series.

* Supplement (follows publication name in pubName field):

- If a reference is in a supplement to the volume listed, or if information about a "part" is needed to distinguish multiple parts with the same page numbering, such information should be put in the REF sub-record.
- A supplement indication should follow the name of the publication and should be preceded by a comma and a space. Supplement should be abbreviated as "SUPPL." If there is a supplement number or letter, it should follow "SUPPL." without an intervening space. A part indication should also follow the name of the publication and be preceded by a comma and a space. A part should be abbreviated as "PT.", and the number or letter should follow without an intervening space.
- If there is both a supplement and a part, their order should reflect the order printed on the work itself.

* Report (follows publication name and any supplement or part information in pubName field):

- If a book has a report designation, the report information should follow the title and precede series information. The name and number of the report is given in parentheses, and the name is preceded by "REPORT:" and a space.

* Reconstruction of publication name:

- The name of the publication is reconstructed by removing any trailing blanks in the pubName field, and concatenating all of the pubName fields from the continuation lines with an intervening space. There are two conditions where no intervening space is added between lines: when the pubName field on a line ends with a hyphen or a period, or when the line ends with a hyphen (-). When the line ends with a period (.), add a space if this is the only period in the entire pubName field; do not add a space if there are two or more periods throughout the pubName field, excluding any periods after the designations "SUPPL", "V", "NO", or "PT".

* Volume, page, and year (volume, page, year fields respectively):

- The REF sub-record type group also contains information about volume, page, and year when applicable.
- In the case of a monograph with multiple volumes which is also in a numbered series, the number in the volume field represents the volume number of the book, not the series. (The volume number of the series is in parentheses with the name of the series, as described above under publication name.)
COLUMNS    DATA TYPE     FIELD         DEFINITION                                
--------------------------------------------------------------------------------
 1 -  6    Record name   "JRNL  "                                                
13 - 16    LString(3)    "REF"                                                   
17 - 18    Continuation  continuation  Allows long publication names.            
20 - 47    LString       pubName       Name of the publication including         
                                       section or series designation.  This is   
                                       the only field of this sub-record which   
                                       may be continued on successive            
                                       sub-records.                              
50 - 51    LString(2)    "V."          Appears in the first sub-record only,     
                                       and only if column 55 is non-blank.       
52 - 55    String        volume        Right-justified blank-filled volume       
                                       information; appears in the first         
                                       sub-record only.                          
57 - 61    String        page          First page of the article; appears in the 
                                       first sub-record only.                    
63 - 66    Integer       year          Year of publication; first sub-record     
                                       only.                                      

5. PUBL

* PUBL contains the name of the publisher and place of publication if the reference is to a book or other non-journal publication. If the non-journal has not yet been published or released, this sub-record is absent.

* The place of publication is listed first, followed by a space, a colon, another space, and then the name of the publisher/issuer. This arrangement is based on the ISBD(M) International Standard Bibliographic Description for Monographic Publications (Rev.Ed., 1987) and AACR2R and is used in public online catalogs in libraries. Details on the contents of PUBL are given below.

* Place of publication:

- Give the place of publication. If the name of the country, state, province, etc. is considered necessary to distinguish the place of publication from others of the same name, or for identification, then follow the city with a comma, a space, and the name of the larger geographic area.
- If there is more than one place of publication, only the first listed will be used. If an online catalog record is used to verify the item, the first place listed there will be used, omitting any brackets. Preference will be given to the cataloging done by the Library of Congress, the National Library of Medicine, and the British Library, in that order.

* Publisher's name (or name of other issuing entity):

- Give the name of the publisher in the shortest form in which it can be understood and identified internationally, according to AACR2R rule 1.4D.
- If there is more than one publisher listed in the publication, only the first will be used in the PDB file. If an online catalog record is used to verify the item, the first place listed there will be used for the name of the publisher. Preference will be given to the cataloging of the Library of Congress, the National Library of Medicine, and the British Library, in that order.

* Ph.D. and other theses:

- Theses are presented in the PUBL record if the degree has been granted and the thesis made available for public consultation by the degree-granting institution.
- The name of the degree-granting institution (the issuing agency) is followed by a space and "(THESIS)".

* Reconstruction of place and publisher:

- The PUBL sub-record type can be reconstructed by removing all trailing blanks in the pub field and concatenating all of the pub fields from the continuation lines with an intervening space. Continued lines do not begin with a space.
COLUMNS    DATA TYPE     FIELD         DEFINITION                                
-------------------------------------------------------------------------------
 1 -  6    Record name   "JRNL  "                                                
13 - 16    LString(4)    "PUBL"                                                  
17 - 18    Continuation  continuation  Allows long publisher and place names.    
20 - 70    LString       pub           City of publication and name of the     
                                       publisher/institution.                    

6. REFN

* REFN is a group of fields which contains encoded references to the citation. No continuation lines are possible. Each piece of coded information has a designated field.

* The American Society for Testing and Materials (ASTM) number is an encoded reference to the journal title. New ASTM codens are assigned by the Chemical Abstracts Service and appear in CASSI and its supplements.

* The country field is blank if the reference was published in more than one country.

* If more than one ISBN is known, select one that matches the individual volume cited (if it happens to be in a set that also has an ISBN for the set). If the reason for multiple ISBNs is that the publication is issued in more than one country, use the ISBN for the country of the first listed place of publication. If there are hardcover and paperback ISBN numbers, use the ISBN for the hardbound version.

* Because some publications do not have an ASTM coden, an ISSN number, or an ISBN number, each publication is assigned a number. This list of numbers, or codens, was established by the Cambridge Crystallographic Data Center (CCDC) and new numbers are assigned by both CCDC and PDB as new publications are added to their respective databases.

* There are two forms of this sub-record type group, depending upon the publication status.

6a. This form of the REFN sub-record type group is used if the citation has not been published.

COLUMNS    DATA TYPE      FIELD      DEFINITION                                   
--------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                                
13 - 16    LString(4)     "REFN"                                                  
67 - 70    LString(4)     "0353"     This is the CCDC/PDB coden for unpublished 
                                     works.  

6b. This form of the REFN sub-record type group is used if the citation has been published.

COLUMNS    DATA TYPE     FIELD         DEFINITION                                
-------------------------------------------------------------------------------
 1 -  6    Record name   "JRNL  "                                                
13 - 16    LString(4)    "REFN"                                                  
20 - 23    LString(4)    "ASTM"                                                  
25 - 30    LString(6)    astm          ASTM devised coden.                       
33 - 34    LString(2)    country       Country of publication code as defined    
                                       in the OCLC/MARC cataloging format        
                                       (optional).                               
36 - 39    LString(4)    "ISBN" or     International Standard Book Number or     
                         "ISSN"        International Standard Serial Number.     
41 - 65    LString       isbn          ISSN or ISBN number (final digit may be   
                                       a letter and may contain one or more      
                                       dashes).                                  
67 - 70    LString(4)    coden         Code from CCDC/PDB coden list.          

Verification/Validation/Value Authority Control

PDB verifies that this record is correctly formatted.

PDB uses MEDLINE to verify the accuracy of references and to obtain information required for CitDB that is not required by the PDB listing. The process of using MEDLINE requires following the National Library of Medicine rules for the transcription of names and titles. Articles in non-MEDLINE journals are verified through other online databases or with the reprint in hand. Verification of book references is done using online cooperative or individual library catalogs.

Citations appearing in JRNL may not also appear in REMARK 1.

Relationships to Other Record Types

The publication cited as the JRNL record may not be repeated in REMARK 1.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
JRNL        AUTH   N.THANKI,J.K.M.RAO,S.I.FOUNDLING,W.J.HOWE,         
JRNL        AUTH 2 A.G.TOMASSELLI,R.L.HEINRIKSON,S.THAISRIVONGS,      
JRNL        AUTH 3 A.WLODAWER                                         
JRNL        TITL   CRYSTAL STRUCTURE OF A COMPLEX OF HIV-1 PROTEASE   
JRNL        TITL 2 WITH A DIHYDROETHYLENE-CONTAINING INHIBITOR:       
JRNL        TITL 3 COMPARISONS WITH MOLECULAR MODELING                
JRNL        REF    TO BE PUBLISHED                                    
JRNL        REFN                                                  0353
JRNL        AUTH   G.FERMI,M.F.PERUTZ,B.SHAANAN,R.FOURME              
JRNL        TITL   THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 
JRNL        TITL 2 1.74 A RESOLUTION                                  
JRNL        REF    J.MOL.BIOL.                   V. 175   159 1984    
JRNL        REFN   ASTM JMOBAK  UK ISSN 0022-2836                 0070

Known Problems

* Interchange of bibliographic information and linking with other databases is hampered by the lack of labels or specific locations for certain types of information or by more than one type of information being in a particular location. This is most likely to occur with books, series, and reports. Some of the points below provide details about the variations and/or blending of information.

* Titles of the publications that require more than 28 characters on the REF line must be continued on subsequent lines. There is some awkwardness due to volume, page, and year appearing on the first REF line, thereby splitting up the title.

* Information about a supplement and its number/letter is presented in the publication's title field (on the REF lines in columns 20 - 47). This sometimes means that the publication's coden has several versions of REF title information.

* When series information for a book is presented, it is added to the REF line. The number of REF lines can become large in some cases because of the 28-column limit for title information in REF.

* There is often an ISBN for a book title and a separate ISSN for the series in which it was published. There is no way to present more than one of these.

* Books that are issued in more than one series are not accommodated.

* Many books are issued in more than one country. The publisher has a separate ISBN number in each country. There is no place to put any additional applicable ISBN numbers, which would be useful in an international database such as the PDB.

* The country code prefix of the ISBN may not match the country of the place of publication that is listed on the PUBL line when a book is published in more than one country.

* Pagination is limited to the beginning page.

* There is no place for listing a reference's accession number in another database.

* MEDLINE truncates the author list after the tenth name.


REMARK

Overview

REMARK records present experimental details, annotations, comments, and information not included in other records. In a number of cases, REMARKs are used to expand the contents of other record types. A new level of structure is being used for some REMARK records. This is expected to facilitate searching and will assist in the conversion to a relational database.

The very first line of every set of REMARK records is used as a spacer to aid in reading.

COLUMNS      DATA TYPE       FIELD          DEFINITION                           
---------------------------------------------------------------------------------
 1 -  6      Record name     "REMARK"           
 8 - 10      Integer         remarkNum      Remark number. It is not an error
                                            for remark n to exist in an entry 
                                            when remark n-1 does not.
12 - 70      LString         empty          Left as white space in first line of
                                            each new remark.  

REMARK 1, 2, and 3, detailed below, are specific for references, resolution, and refinement, respectively.

REMARK 1

REMARK 1 lists important publications related to the structure presented in the entry. These citations are chosen by the depositor. They are listed in reverse-chronological order. Citations are not repeated from the JRNL records. After the first blank record and the REFERENCE sub-record, the sub-record types for REMARK 1 are the same as in the JRNL sub-record types. For details, see the JRNL section.

PDB is in the process of linking and/or adding references to CitDB, the literature database of the Genome Data Base (available at URL http://gdbwww.gdb.org/gdb-bin/genera/genera/citation/Citation).

Record Format and Details

As with all other remarks, the first line is empty and is used as a spacer.

The following tables are used to describe the sub-record types of REMARK 1.

1. REFERENCE

Each reference is preceded by a line indicating the reference number in the entry.

COLUMNS        DATA TYPE       FIELD              DEFINITION                     
--------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          
10             LString(1)      "1"                                               
12 - 20        LString(9)      "REFERENCE"                                       
22 - 70        Integer         refNum             Reference number. Starts with 
                                                  1 and increments by 1.        

2. AUTH

AUTH contains the list of authors of the reference.

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
-------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          
10             LString(1)      "1"                                               
13 - 16        LString(4)      "AUTH"         Appears on all continuation        
                                                  records.                           
17 - 18        Continuation    continuation   Allows a long list of authors.     
20 - 70        List            authorList     List of the authors.               

See JRNL AUTH for details.

3. TITL

TITL specifies the title of the reference.

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
-------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          
10             LString(1)      "1"                                               
13 - 16        LString(4)      "TITL"         Appears on all continuation        
                                              records.                           
17 - 18        Continuation    continuation   Permits long titles.               
20 - 70        LString         title          Title of the article.              

See JRNL TITL for details.

4. EDIT

EDIT appears if editors are associated with a non-journal reference.

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
-------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          
10             LString(1)      "1"                                               
13 - 16        LString(4)      "EDIT"         Appears on all continuation        
                                              records.                           
17 - 18        Continuation    continuation   Permits long list of editors.      
20 - 70        LString         editorList     List of the editors.               

See JRNL EDIT for details.

5. REF

REF is a group of fields which contains the name of the publication.

5a. If it has not yet been published, the REF sub-record type has the form:

COLUMNS    DATA TYPE      FIELD                   DEFINITION                      
-------------------------------------------------------------------------------
 1 -  6    Record name    "REMARK"                                                
10         LString(1)     "1"                                                     
13 - 16    LString(3)     "REF"                                                   
20 - 34    LString(15)    "TO BE PUBLISHED"                                       

At the present time, there is no formal mechanism in place for monitoring the subsequent publication of referenced papers. PDB relies upon the depositor to provide reference update information since preliminary information can change by the time of actual publication.

5b. If the reference has been published, then the REF sub-record type group contains information about the name of the publication, supplement, report, volume, page, and year, in the appropriate fields.

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
---------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          
10             LString(1)      "1"                                               
13 - 16        LString(3)      "REF"                                             
17 - 18        Continuation    continuation   Permits long publication names.     
20 - 47        LString         pubName        Name of the publication including  
                                              section or series designation.     
                                              This is the only field of this     
                                              record which may be continued on    
                                              successive records.                 
50 - 51        LString(2)      "V."           Appears in the first record only,   
                                              and only if column 55 is filled in. 
52 - 55        String          volume         Right-justified blank-filled volume 
                                              information; appears in the first   
                                              sub-record only.                    
57 - 61        String          page           First page of the article; appears 
                                              in the first sub-record only.       
63 - 66        Integer         year           Year of publication, first record   
                                              only.                               

See JRNL REF for details.

6. PUBL

PUBL contains the name of the publisher and place of publication if the reference is to a book or other non-journal publication. If the reference has not yet been published or released, this sub-record is absent.

COLUMNS        DATA TYPE       FIELD          DEFINITION                          
---------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                           
10             LString(1)      "1"                                                
13 - 16        LString(4)      "PUBL"                                             
17 - 18        Continuation    continuation   Permits long publisher and city     
                                              information.                        
20 - 70        LString         pub            Name of the publisher and city of   
                                              publication.                        

See JRNL PUBL for details.

7. REFN

REFN is a group of fields which contains encoded references to the citation.

7a. If the citation has not been published, this form of the REFN sub-record type group is used.

COLUMNS    DATA TYPE      FIELD        DEFINITION                                 
-------------------------------------------------------------------------------
 1 -  6    Record name    "REMARK"                                                
10         LString(1)     "1"                                                     
13 - 16    LString(4)     "REFN"                                                  
67 - 70    LString(4)     "0353"       This is the PDB coden for unpublished      
                                       works.                                     

7b. If the citation has been published, this form of the REFN sub-record type group is used.

COLUMNS        DATA TYPE        FIELD            DEFINITION                      
--------------------------------------------------------------------------------
 1 -  6        Record name      "REMARK"                                         
10             LString(1)       "1"                                              
13 - 16        LString(4)       "REFN"                                           
20 - 23        LString(4)       "ASTM"           Blank if reference is not       
                                                 serialized.                     
25 - 30        LString          astm             Code from the ASTM file.        
33 - 34        LString          country          2-digit abbreviation for        
                                                 country of publication.         
36 - 39        LString(4)       "ISBN" or                                        
                                "ISSN"                                           
41 - 65        LString          isbn             ISSN or ISBN number.            
68 - 70        LString(4)       coden            Number from Cambridge           
                                                 Crystallographic Data Center    
                                                 coden list, or assigned by the  
                                                 PDB.                            

See JRNL REFN for details.

Verification/Validation/Value Authority Control

PDB verifies that this record is correctly formatted.

PDB uses MEDLINE to verify the accuracy of references and to obtain information required for CitDB that is not required by the PDB listing. The process of using MEDLINE requires following the National Library of Medicine rules for the transcription of names and titles. Articles in non-MEDLINE journals are verified through other online databases or with the reprint in hand. Verification of book references is done using online cooperative or individual library catalogs.

Citations appearing in REMARK 1 may not appear in JRNL.

Relationships to Other Record Types

Citations appearing in REMARK 1 may not appear in JRNL.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   A.M.BONVIN,J.A.RULLMANN,R.M.LAMERICHS,R.BOELENS,
REMARK   1  AUTH 2 R.KAPTEIN
REMARK   1  TITL   "ENSEMBLE" ITERATIVE RELAXATION MATRIX APPROACH:
REMARK   1  TITL 2 A NEW NMR REFINEMENT PROTOCOL APPLIED TO THE
REMARK   1  TITL 3 SOLUTION STRUCTURE OF CRAMBIN
REMARK   1  REF    PROTEINS: STRUCT.,FUNCT.,     V.  15   385 1993
REMARK   1  REF  2 GENET.
REMARK   1  REFN   ASTM PSFGEY  US ISSN 0887-3585                 0867
REMARK   1 REFERENCE 2
REMARK   1  AUTH   J.A.C.RULLMANN,A.M.J.J.BONVIN,R.BOELENS,R.KAPTEIN
REMARK   1  TITL   STRUCTURE DETERMINATION BY NMR - APPLICATION TO
REMARK   1  TITL 2 CRAMBIN
REMARK   1  EDIT   D.M.SOUMPASIS,T.M.JOVIN
REMARK   1  REF    COMPUTATION OF BIOMOLECULAR              1 1992
REMARK   1  REF  2 STRUCTURES; ACHIEVEMENTS,
REMARK   1  REF  3 PROBLEMS, AND PERSPECTIVES
REMARK   1  PUBL   BERLIN : SPRINGER-VERLAG 
REMARK   1  REFN                GW ISBN 3540559515                2010
REMARK   1 REFERENCE 3
REMARK   1  AUTH   R.M.J.M.LAMERICHS
REMARK   1  REF    2D NMR STUDIES OF                          1989
REMARK   1  REF  2 BIOMOLECULES: PROTEIN 
REMARK   1  REF  3 STRUCTURE AND PROTEIN-DNA 
REMARK   1  REF  4 INTERACTIONS
REMARK   1  PUBL   UTRECHT : UNIVERSITY OF UTRECHT (THESIS)
REMARK   1  REFN                NE                                2011
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   G.FERMI,M.F.PERUTZ
REMARK   1  REF    HAEMOGLOBIN AND MYOGLOBIN                  1981
REMARK   1  REF  2 (IN: ATLAS OF MOLECULAR
REMARK   1  REF  3 STRUCTURES IN BIOLOGY, V.2)
REMARK   1  PUBL   OXFORD : CLARENDON PRESS
REMARK   1  REFN                   ISBN 0-19-854706-4             0986

Known Problems

See JRNL for a listing of problems associated with references.


REMARK 2

REMARK 2 states the highest resolution, in Angstroms, that was used in building the model. As with all the remarks, the first REMARK 2 record is empty and is used as a spacer.

Record Format and Details

* The second REMARK 2 record has one of two formats. The first is used for diffraction studies, the second for other types of experiments in which resolution is not relevant, e.g., NMR and theoretical modeling.

* For diffraction experiments:

COLUMNS        DATA TYPE       FIELD               DEFINITION                     
--------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                           
10             LString(1)      "2"                                                
12 - 22        LString(11)     "RESOLUTION."                                      
23 - 27        Real(5.2)       resolution          Resolution.                    
29 - 38        LString(10)     "ANGSTROMS."                                       

REMARK 2 when not a diffraction experiment:

COLUMNS        DATA TYPE       FIELD                            DEFINITION        
--------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                           
10             LString(1)      "2"                                                
12 - 38        LString(28)     "RESOLUTION. NOT APPLICABLE."                     
41 - 70        String          comment                          Comment.          

* Additional explanatory text may be included starting with the third line of the REMARK 2 record. For example, depositors may wish to qualify the resolution value provided due to unusual experimental conditions.

COLUMNS        DATA TYPE       FIELD               DEFINITION                     
-------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                           
10             LString(1)      "2"                                                
12 - 22        LString(11)     "RESOLUTION."                                      
24 - 70        String          comment             Comment.                       

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK   2                                                            
REMARK   2 RESOLUTION. 1.74 ANGSTROMS.                                
REMARK   2                                                            
REMARK   2 RESOLUTION. NOT APPLICABLE.                                
REMARK   2                                                            
REMARK   2 RESOLUTION. NOT APPLICABLE.                                
REMARK   2 THIS EXPERIMENT WAS CARRIED OUT USING FLUORESCENCE TRANSFER
REMARK   2 AND THEREFORE NO RESOLUTION CAN BE CALCULATED.


REMARK 3

Overview

REMARK 3 presents information on refinement program(s) used and the related statistics. For non-diffraction studies, REMARK 3 is used to describe any refinement done, but its format in those cases is mostly free text.

If more than one refinement package was used, they may be named in "OTHER REFINEMENT REMARKS". However, Remark 3 statistics are given for the final refinement run.

Refinement packages are being enhanced to output PDB REMARK 3. A token: value template style facilitates parsing. Spacer REMARK 3 lines are interspersed for visually organizing the information.

The templates below have been adopted in consultation with program authors. PDB is continuing this dialogue with program authors, and expects the library of PDB records output by the programs to greatly increase in the near future.

Instead of providing a Record Format table, each template is given as it appears in PDB entries.

Details

* The value "NULL" is given when there is no data available for a particular token.

Refinement using X-PLOR

This remark will be output by X-PLOR(online) for direct submission to PDB. Structures done using earlier versions of X-PLOR will contain the same template, but with many of the data items containing "NULL".

Template

REMARK   3
REMARK   3 REFINEMENT. 
REMARK   3   PROGRAM     : X-PLOR 
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT. 
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 
REMARK   3   NUMBER OF REFLECTIONS             : 
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT. 
REMARK   3   CROSS-VALIDATION METHOD          : 
REMARK   3   FREE R VALUE TEST SET SELECTION  : 
REMARK   3   R VALUE            (WORKING SET) : 
REMARK   3   FREE R VALUE                     : 
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 
REMARK   3   FREE R VALUE TEST SET COUNT      : 
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN. 
REMARK   3   TOTAL NUMBER OF BINS USED           : 
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 
REMARK   3   BIN R VALUE           (WORKING SET) : 
REMARK   3   BIN FREE R VALUE                    : 
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. 
REMARK   3   PROTEIN ATOMS            : 
REMARK   3   NUCLEIC ACID ATOMS       : 
REMARK   3   HETEROGEN ATOMS          : 
REMARK   3   SOLVENT ATOMS            : 
REMARK   3
REMARK   3  B VALUES. 
REMARK   3   FROM WILSON PLOT           (A**2) : 
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 
REMARK   3   OVERALL ANISOTROPIC B VALUE. 
REMARK   3    B11 (A**2) : 
REMARK   3    B22 (A**2) : 
REMARK   3    B33 (A**2) : 
REMARK   3    B12 (A**2) : 
REMARK   3    B13 (A**2) : 
REMARK   3    B23 (A**2) : 
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR. 
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 
REMARK   3   ESD FROM SIGMAA              (A) : 
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR. 
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 
REMARK   3   ESD FROM C-V SIGMAA          (A) : 
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES. 
REMARK   3   BOND LENGTHS                 (A) : 
REMARK   3   BOND ANGLES            (DEGREES) : 
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 
REMARK   3   IMPROPER ANGLES        (DEGREES) : 
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : 
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) :       ; 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) :       ; 
REMARK   3   SIDE-CHAIN BOND              (A**2) :       ; 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) :       ; 
REMARK   3
REMARK   3  NCS MODEL : 
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) :       ; 
REMARK   3   GROUP  1  B-FACTOR           (A**2) :       ; 
REMARK   3   GROUP  2  POSITIONAL            (A) :       ; 
REMARK   3   GROUP  2  B-FACTOR           (A**2) :       ; 
REMARK   3   GROUP  3  POSITIONAL            (A) :       ; 
REMARK   3   GROUP  3  B-FACTOR           (A**2) :       ; 
REMARK   3   GROUP  4  POSITIONAL            (A) :       ; 
REMARK   3   GROUP  4  B-FACTOR           (A**2) :       ; 
REMARK   3
REMARK   3  PARAMETER FILE  1  : 
REMARK   3  PARAMETER FILE  2  : 
REMARK   3  PARAMETER FILE  3  : 
REMARK   3  PARAMETER FILE  4  : 
REMARK   3  PARAMETER FILE  5  : 
REMARK   3  PARAMETER FILE  6  : 
REMARK   3  TOPOLOGY FILE  1   : 
REMARK   3  TOPOLOGY FILE  2   : 
REMARK   3  TOPOLOGY FILE  3   : 
REMARK   3  TOPOLOGY FILE  4   : 
REMARK   3  TOPOLOGY FILE  5   : 
REMARK   3  TOPOLOGY FILE  6   : 
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: 
Refinement using NUCLSQ

Template

REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : NUCLSQ
REMARK   3   AUTHORS     : WESTHOF,DUMAS,MORAS 
REMARK   3
REMARK   3  DATA USED IN REFINEMENT. 
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 
REMARK   3   COMPLETENESS FOR RANGE        (%) : 
REMARK   3   NUMBER OF REFLECTIONS             : 
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : 
REMARK   3   FREE R VALUE TEST SET SELECTION  : 
REMARK   3   R VALUE     (WORKING + TEST SET) :
REMARK   3   R VALUE            (WORKING SET) :
REMARK   3   FREE R VALUE                     :
REMARK   3   FREE R VALUE TEST SET SIZE   (%) :
REMARK   3   FREE R VALUE TEST SET COUNT      :
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) :
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) :
REMARK   3   FREE R VALUE                  (NO CUTOFF) :
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 
REMARK   3  
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            :
REMARK   3   NUCLEIC ACID ATOMS       :
REMARK   3   HETEROGEN ATOMS          :
REMARK   3   SOLVENT ATOMS            :
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 
REMARK   3    B22 (A**2) : 
REMARK   3    B33 (A**2) : 
REMARK   3    B12 (A**2) : 
REMARK   3    B13 (A**2) : 
REMARK   3    B23 (A**2) : 
REMARK   3  
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 
REMARK   3   ESD FROM SIGMAA              (A) : 
REMARK   3   LOW RESOLUTION CUTOFF        (A) :
REMARK   3 
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   DISTANCE RESTRAINTS.                    RMS     SIGMA
REMARK   3    SUGAR-BASE BOND DISTANCE        (A) :       ; 
REMARK   3    SUGAR-BASE BOND ANGLE DISTANCE  (A) :       ; 
REMARK   3    PHOSPHATE BONDS DISTANCE        (A) :       ;  
REMARK   3    PHOSPHATE BOND ANGLE, H-BOND    (A) :       ; 
REMARK   3 
REMARK   3   PLANE RESTRAINT                  (A) :       ;  
REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) :       ;  
REMARK   3 
REMARK   3   NON-BONDED CONTACT RESTRAINTS. 
REMARK   3    SINGLE TORSION CONTACT          (A) :       ;  
REMARK   3    MULTIPLE TORSION CONTACT        (A) :       ;  
REMARK   3 
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA 
REMARK   3   SUGAR-BASE BONDS             (A**2) :       ;  
REMARK   3   SUGAR-BASE ANGLES            (A**2) :       ;  
REMARK   3   PHOSPHATE BONDS              (A**2) :       ;  
REMARK   3   PHOSPHATE BOND ANGLE, H-BOND (A**2) :       ;  
REMARK   3 
REMARK   3  OTHER REFINEMENT REMARKS: 
Refinement using PROLSQ, CCP4, PROFFT, GPRLSA, and related programs

Template

REMARK   3 
REMARK   3 REFINEMENT. 
REMARK   3   PROGRAM     : 
REMARK   3   AUTHORS     : 
REMARK   3 
REMARK   3  DATA USED IN REFINEMENT.  
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) :  
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) :  
REMARK   3   DATA CUTOFF            (SIGMA(F)) :  
REMARK   3   COMPLETENESS FOR RANGE        (%) :  
REMARK   3   NUMBER OF REFLECTIONS             :  
REMARK   3 
REMARK   3  FIT TO DATA USED IN REFINEMENT. 
REMARK   3   CROSS-VALIDATION METHOD          : 
REMARK   3   FREE R VALUE TEST SET SELECTION  : 
REMARK   3   R VALUE     (WORKING + TEST SET) : 
REMARK   3   R VALUE            (WORKING SET) : 
REMARK   3   FREE R VALUE                     : 
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 
REMARK   3   FREE R VALUE TEST SET COUNT      : 
REMARK   3 
REMARK   3  FIT/AGREEMENT OF MODEL WITH ALL DATA. 
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 
REMARK   3   FREE R VALUE                  (NO CUTOFF) :  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) :  
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) :  
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) :  
REMARK   3   
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. 
REMARK   3   PROTEIN ATOMS            : 
REMARK   3   NUCLEIC ACID ATOMS       : 
REMARK   3   HETEROGEN ATOMS          : 
REMARK   3   SOLVENT ATOMS            : 
REMARK   3 
REMARK   3  B VALUES. 
REMARK   3   FROM WILSON PLOT           (A**2) :  
REMARK   3   MEAN B VALUE      (OVERALL, A**2) :  
REMARK   3   OVERALL ANISOTROPIC B VALUE. 
REMARK   3    B11 (A**2) :  
REMARK   3    B22 (A**2) :  
REMARK   3    B33 (A**2) :  
REMARK   3    B12 (A**2) :  
REMARK   3    B13 (A**2) :  
REMARK   3    B23 (A**2) :  
REMARK   3   
REMARK   3  ESTIMATED COORDINATE ERROR. 
REMARK   3   ESD FROM LUZZATI PLOT        (A) :  
REMARK   3   ESD FROM SIGMAA              (A) :  
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 
REMARK   3  
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES. 
REMARK   3   DISTANCE RESTRAINTS.                    RMS    SIGMA 
REMARK   3    BOND LENGTH                     (A) :       ;  
REMARK   3    ANGLE DISTANCE                  (A) :       ; 
REMARK   3    INTRAPLANAR 1-4 DISTANCE        (A) :       ;  
REMARK   3    H-BOND OR METAL COORDINATION    (A) :       ;  
REMARK   3 
REMARK   3   PLANE RESTRAINT                  (A) :       ;  
REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) :       ;  
REMARK   3 
REMARK   3   NON-BONDED CONTACT RESTRAINTS. 
REMARK   3    SINGLE TORSION                  (A) :       ;  
REMARK   3    MULTIPLE TORSION                (A) :       ;  
REMARK   3    H-BOND (X...Y)                  (A) :       ;  
REMARK   3    H-BOND (X-H...Y)                (A) :       ;  
REMARK   3 
REMARK   3   CONFORMATIONAL TORSION ANGLE RESTRAINTS. 
REMARK   3    SPECIFIED                 (DEGREES) :       ;  
REMARK   3    PLANAR                    (DEGREES) :       ;  
REMARK   3    STAGGERED                 (DEGREES) :       ;  
REMARK   3    TRANSVERSE                (DEGREES) :       ;  
REMARK   3 
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA 
REMARK   3   MAIN-CHAIN BOND              (A**2) :       ;  
REMARK   3   MAIN-CHAIN ANGLE             (A**2) :       ;  
REMARK   3   SIDE-CHAIN BOND              (A**2) :       ;  
REMARK   3   SIDE-CHAIN ANGLE             (A**2) :       ;  
REMARK   3 
REMARK   3  OTHER REFINEMENT REMARKS: 
Refinement using SHELXL
This remark will be output by SHELXL-96 for direct submission to PDB. Structures done using earlier versions of SHELX will use the same template, but with many of the data items containing "NULL".

Template

REMARK   3
REMARK   3 REFINEMENT.
REMARK   3  PROGRAM     : SHELXL
REMARK   3  AUTHORS     : G.M.SHELDRICK
REMARK   3
REMARK   3 DATA USED IN REFINEMENT.
REMARK   3  RESOLUTION RANGE HIGH (ANGSTROMS) : 
REMARK   3  RESOLUTION RANGE LOW  (ANGSTROMS) :
REMARK   3  DATA CUTOFF            (SIGMA(F)) : 
REMARK   3  COMPLETENESS FOR RANGE        (%) :
REMARK   3  CROSS-VALIDATION METHOD           : 
REMARK   3  FREE R VALUE TEST SET SELECTION   : 
REMARK   3
REMARK   3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK   3  R VALUE   (WORKING + TEST SET, NO CUTOFF) : 
REMARK   3  R VALUE          (WORKING SET, NO CUTOFF) : 
REMARK   3  FREE R VALUE                  (NO CUTOFF) : 
REMARK   3  FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 
REMARK   3  FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 
REMARK   3  TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 
REMARK   3
REMARK   3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3  R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 
REMARK   3  R VALUE          (WORKING SET, F>4SIG(F)) : 
REMARK   3  FREE R VALUE                  (F>4SIG(F)) : 
REMARK   3  FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 
REMARK   3  FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : 
REMARK   3  TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 
REMARK   3
REMARK   3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3  PROTEIN ATOMS      : 
REMARK   3  NUCLEIC ACID ATOMS : 
REMARK   3  HETEROGEN ATOMS    : 
REMARK   3  SOLVENT ATOMS      : 
REMARK   3
REMARK   3 MODEL REFINEMENT.
REMARK   3  OCCUPANCY SUM OF NON-HYDROGEN ATOMS      :
REMARK   3  OCCUPANCY SUM OF HYDROGEN ATOMS          : 
REMARK   3  NUMBER OF DISCRETELY DISORDERED RESIDUES : 
REMARK   3  NUMBER OF LEAST-SQUARES PARAMETERS       : 
REMARK   3  NUMBER OF RESTRAINTS                     : 
REMARK   3
REMARK   3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3  BOND LENGTHS                         (A) : 
REMARK   3  ANGLE DISTANCES                      (A) : 
REMARK   3  SIMILAR DISTANCES (NO TARGET VALUES) (A) : 
REMARK   3  DISTANCES FROM RESTRAINT PLANES      (A) : 
REMARK   3  ZERO CHIRAL VOLUMES               (A**3) : 
REMARK   3  NON-ZERO CHIRAL VOLUMES           (A**3) : 
REMARK   3  ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 
REMARK   3  RIGID-BOND ADP COMPONENTS         (A**2) : 
REMARK   3  SIMILAR ADP COMPONENTS            (A**2) :
REMARK   3  APPROXIMATELY ISOTROPIC ADPS      (A**2) : 
REMARK   3
REMARK   3 BULK SOLVENT MODELING.
REMARK   3  METHOD USED: 
REMARK   3
REMARK   3 STEREOCHEMISTRY TARGET VALUES : 
REMARK   3  SPECIAL CASE:
REMARK   3
REMARK   3 OTHER REFINEMENT REMARKS:
Refinement using TNT

Template

REMARK   3 
REMARK   3 REFINEMENT. 
REMARK   3   PROGRAM     : TNT  
REMARK   3   AUTHORS     : TRONRUD,TEN EYCK,MATTHEWS 
REMARK   3 
REMARK   3  DATA USED IN REFINEMENT.  
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) :
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) :
REMARK   3   DATA CUTOFF            (SIGMA(F)) :
REMARK   3   COMPLETENESS FOR RANGE        (%) : 
REMARK   3   NUMBER OF REFLECTIONS             : 
REMARK   3 
REMARK   3  USING DATA ABOVE SIGMA CUTOFF. 
REMARK   3   CROSS-VALIDATION METHOD          :  
REMARK   3   FREE R VALUE TEST SET SELECTION  :  
REMARK   3   R VALUE     (WORKING + TEST SET) : 
REMARK   3   R VALUE            (WORKING SET) : 
REMARK   3   FREE R VALUE                     : 
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 
REMARK   3   FREE R VALUE TEST SET COUNT      : 
REMARK   3 
REMARK   3  USING ALL DATA, NO SIGMA CUTOFF. 
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 
REMARK   3   FREE R VALUE                  (NO CUTOFF) :  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) :  
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) :  
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) :  
REMARK   3 
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. 
REMARK   3   PROTEIN ATOMS            :  
REMARK   3   NUCLEIC ACID ATOMS       :  
REMARK   3   OTHER ATOMS          :  
REMARK   3 
REMARK   3  WILSON B VALUE (FROM FCALC, A**2) :  
REMARK   3 
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.    RMS    WEIGHT  COUNT 
REMARK   3   BOND LENGTHS                 (A) :       ;       ;  
REMARK   3   BOND ANGLES            (DEGREES) :       ;       ;  
REMARK   3   TORSION ANGLES         (DEGREES) :       ;       ;  
REMARK   3   PSEUDOROTATION ANGLES  (DEGREES) :       ;       ;  
REMARK   3   TRIGONAL CARBON PLANES       (A) :       ;       ;  
REMARK   3   GENERAL PLANES               (A) :       ;       ;  
REMARK   3   ISOTROPIC THERMAL FACTORS (A**2) :       ;       ;  
REMARK   3   NON-BONDED CONTACTS          (A) :       ;       ;  
REMARK   3 
REMARK   3  INCORRECT CHIRAL-CENTERS (COUNT) :  
REMARK   3 
REMARK   3  BULK SOLVENT MODELING. 
REMARK   3   METHOD USED :  
REMARK   3   KSOL        :  
REMARK   3   BSOL        :  
REMARK   3 
REMARK   3  RESTRAINT LIBRARIES. 
REMARK   3   STEREOCHEMISTRY :  
REMARK   3   ISOTROPIC THERMAL FACTOR RESTRAINTS :  
REMARK   3 
REMARK   3  OTHER REFINEMENT REMARKS: 
Non-diffraction studies
Until standard refinement remarks are adopted for non-diffraction studies, their refinement details are given in REMARK 3, but its format will consist totally of free text beginning on the sixth line of the remark.

Template

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK   3 
REMARK   3 REFINEMENT.                                                
REMARK   3   PROGRAM     : 
REMARK   3   AUTHORS     : 
REMARK   3                                                            
REMARK   3 FREE TEXT                                     

Example

         1         2         3         4         5         6         7
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REMARK   3 
REMARK   3 REFINEMENT.                                                
REMARK   3   PROGRAM     : X-PLOR 3.1                    
REMARK   3   AUTHORS     : BRUNGER                       
REMARK   3                                                            
REMARK   3 STRUCTURAL STATISTICS:                                     
REMARK   3                                      25 SA                 
REMARK   3                                      STRUCTURES  SAAVEMIN  
REMARK   3  RMS DEVIATIONS FROM EXP. RESTRAINTS[A]                    
REMARK   3   NOE DISTANCE RESTRAINTS (1430)   0.0451 A       0.044 A  
REMARK   3   DIHEDRAL ANGLE RESTRAINTS (130)  0.551 DEG      0.660 DEG
REMARK   3  DEVIATIONS FROM IDEAL GEOMETRY                            
REMARK   3   BONDS                            0.004  A       0.004 A  
REMARK   3   ANGLES                           0.661 DEG      0.650 DEG
REMARK   3   IMPROPERS                        0.371 DEG      0.380 DEG
REMARK   3  X-PLOR ENERGIES (IN KCAL MOL-1)[B]                        
REMARK   3   ENOE                             167            158      
REMARK   3   ECDIH                            2.6            3.4      
REMARK   3   ENCS                             0.01           0.01     
REMARK   3   EREPEL                           54             50       
REMARK   3   EBOND                            36             33       
REMARK   3   EANGLE                           263            256      
REMARK   3   EIMPROPER                        22             23       
REMARK   3   ETOTAL                           545            523      
REMARK   3  ATOMIC RMS DIFFERENCES[C]                                 
REMARK   3  BACKBONE(N, CA, C') + LIGAND ATOMS   0.53+/-0.09 A        
REMARK   3  ALL HEAVY ATOMS                      0.91+/-0.08 A        

REMARK 4 - 999

Overview

REMARKs following the refinement remark consist of free text annotation, predefined boilerplate remarks, and token: value pair styled templates. PDB is beginning to organize the most often used remarks, and assign numbers and topics to them.

Presented here is the scheme being followed in the remark section of PDB files. The PDB expects to continue to adopt standard text or tables for certain remarks, as details are worked out.

Record Format and Details

* Non-standard remark annotations, or those with no clearly-defined topic or assigned remark number, appear with remark number 6 or greater, but less than remark number 100.

* Note that A, B, N, X, Y, and Z are used to represent variables in the following examples.

* As with all other remarks, the first line of each remark is empty and is used as a spacer.

REMARK 4, Format

Entries released after April 15, 1996 will comply with Format Version 2.0, described in this document. Conversion of older entries to this format will begin in the fall of 1996.
Entries conforming to the format described in this or future PDB Contents Guides will have a remark of the following form within them:
Remark 4 is mandatory in entry if released after April 15, 1996.

Template

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REMARK   4
REMARK   4 XXXX COMPLIES WITH FORMAT V. N.M, DD-MMM-YYYY

XXXX refers to the ID code of the entry.
N.M refers to the version number.
DD-MMM-YYYY refers to the release date of that version of the format. DD is a number 01 through 31, MMM is a 3 letter abbreviation for the month, and YYYY is the year.

Example

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REMARK   4
REMARK   4 1ABC COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996

REMARK 5, Warning

Remark 5 repeats information presented on the CAVEAT record, which warns of severe errors in an entry. It also presents depositors' remarks of a cautionary nature, such as noting regions of poorly defined density.

Template

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REMARK   5
REMARK   5 WARNING
REMARK   5 XXXX: FREE TEXT GOES HERE.

XXXX refers to the ID code of the entry.

Example

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REMARK   5
REMARK   5 WARNING
REMARK   5 1ABC: THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS
REMARK   5 UNCORRECTABLE AT THIS TIME.

REMARK 6 - 99, not assigned

Non-standard remark annotations, or those with no clearly defined topic or assigned remark number appear with remark number 6 or greater, but less than remark number 100.

REMARK 100 - 199, Nucleic acids

These remarks are used in nucleic acid structures processed by the Nucleic Acid Database.

Template

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REMARK 100 
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY THE NUCLEIC ACID DATABASE  
REMARK 100 ON DD-MMM-YYYY. 
REMARK 100 THE NDB ID CODE IS NNNNNN. 

For modified residues

Remark 101 is mandatory if substituted nucleic acid residues exit.

Template

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REMARK 101
REMARK 101 RESIDUE   X Y   N HAS XXX    BONDED TO AB. 
REMARK 101 RESIDUE   X Y   N HAS XXX    BONDED TO AB. 

X is the modified residue name, Y is the chain identifier, N is the sequence number, XXX is the name of the modifier, A is the atom name and B the sequence number of the atom carrying the modifier.

Example

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REMARK 101
REMARK 101 RESIDUE   G A   4 HAS CH3    BONDED TO O6.
REMARK 101 RESIDUE   G B  16 HAS CH3    BONDED TO O6.

For base mispairings

Remark 102 is mandatory if mispaired bases exist and Watson-Crick H-bonding is present.

Template

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REMARK 102
REMARK 102 BASES   A B  NN AND   X Y  ZZ ARE MISPAIRED. 
REMARK 102 BASES   A B  NN AND   X Y  ZZ ARE MISPAIRED. 
REMARK 102 ALL OTHER HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
REMARK 102 FOLLOW THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
REMARK 102 PATTERN AND THEY HAVE NOT BEEN PRESENTED ON *CONECT*
REMARK 102 RECORDS IN THIS ENTRY. 

A is the residue name, B the chain identifier, and NN the sequence number of first base, X is the residue name, Y the chain id, and ZZ the sequence number of the second base.

Example

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REMARK 102
REMARK 102 BASES   G A   4 AND   A B  21 ARE MISPAIRED. 
REMARK 102 BASES   A A   9 AND   G B  16 ARE MISPAIRED. 
REMARK 102 ALL OTHER HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
REMARK 102 FOLLOW THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
REMARK 102 PATTERN AND THEY HAVE NOT BEEN PRESENTED ON *CONECT*
REMARK 102 RECORDS IN THIS ENTRY. 

For structures containing inosine

Inosine is treated like a standard residue, however, entries containing inosine also include remarks 103 and 104.

Remark 103 is mandatory if non-Watson-Crick H-bonding is present for specific interactions.

Template

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REMARK 103
REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE
REMARK 103 FOLLOWING ATOMS: 
REMARK 103  AB   I X   N   AND  AB   Z X  NN
REMARK 103  AB   I X   N   AND  AB   Z X  NN
REMARK 103 ALL OTHER HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
REMARK 103 FOLLOW THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
REMARK 103 PATTERN AND THEY HAVE NOT BEEN PRESENTED ON *CONECT*
REMARK 103 RECORDS IN THIS ENTRY. 

AB is the atom name, I the residue name inosine, X the chain identifier, and N the sequence number of inosine, and AB is the atom name, Z the residue name, X the chain identifier, and NN the sequence number of the base which is paired with inosine.

Remark 104 is mandatory if inosine exists.

Template

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REMARK 104
REMARK 104 RESIDUE I X   N IS INOSINE. 
REMARK 104 RESIDUE I X   N IS INOSINE. 

X is the chain identifier and N the sequence number.

Example

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REMARK 103
REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE
REMARK 103 FOLLOWING ATOMS: 
REMARK 103  N1   I A   1   AND  N3   C B  16
REMARK 103  O6   I A   1   AND  N4   C B  16
REMARK 103  N1   I A   3   AND  N3   C B  14
REMARK 103  O6   I A   3   AND  N4   C B  14
REMARK 103 ALL OTHER HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
REMARK 103 FOLLOW THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
REMARK 103 PATTERN AND THEY HAVE NOT BEEN PRESENTED ON CONECT
REMARK 103 RECORDS IN THIS ENTRY.
REMARK 104
REMARK 104 RESIDUE I A   1 IS INOSINE. 
REMARK 104 RESIDUE I A   3 IS INOSINE. 

For nucleic acid entries

Remark 105 is mandatory if nucleic acids exist in an entry.

Template

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REMARK 105 
REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS  
REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY    
REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS.  THE RING     
REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.

For non-mismatched structures

Remark 106 is mandatory if hydrogen bonding is Watson-Crick.

Template

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REMARK 106
REMARK 106 THE HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY FOLLOW
REMARK 106 THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING PATTERN.
REMARK 106 THEY HAVE NOT BEEN PRESENTED ON *CONECT* RECORDS IN THIS
REMARK 106 ENTRY.

REMARK 200-250, Experimental Details

Remarks in this range present the data collection details for the data which resulted in the refinement statistics of REMARK 3. They provide information on the structure determination experiment, which may have been done by diffraction, NMR, theoretical modelling, or some other technique.
The "NULL" value will be used if the data for a token is not supplied by the depositor.

REMARK 200, X-ray Diffraction Experimental Details

To be used for single crystal, fiber, or polycrystalline X-ray diffraction experiments.
Remark 200 is mandatory if x-ray.

Template

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REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 
REMARK 200  TEMPERATURE           (KELVIN) : 
REMARK 200  PH                             : 
REMARK 200  NUMBER OF CRYSTALS USED        : 
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : 
REMARK 200  RADIATION SOURCE               : 
REMARK 200  BEAMLINE                       : 
REMARK 200  X-RAY GENERATOR MODEL          : 
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : 
REMARK 200  WAVELENGTH OR RANGE        (A) : 
REMARK 200  MONOCHROMATOR                  : 
REMARK 200  OPTICS                         : 
REMARK 200
REMARK 200  DETECTOR TYPE                  : 
REMARK 200  DETECTOR MANUFACTURER          : 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : 
REMARK 200  DATA SCALING SOFTWARE          : 
REMARK 200  
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 
REMARK 200  RESOLUTION RANGE HIGH      (A) : 
REMARK 200  RESOLUTION RANGE LOW       (A) : 
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 
REMARK 200  DATA REDUNDANCY                : 
REMARK 200  R MERGE                    (I) : 
REMARK 200  R SYM                      (I) : 
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 
REMARK 200  COMPLETENESS FOR SHELL     (%) : 
REMARK 200  DATA REDUNDANCY IN SHELL       : 
REMARK 200  R MERGE FOR SHELL          (I) : 
REMARK 200  R SYM FOR SHELL            (I) : 
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 
REMARK 200
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: 
REMARK 200 SOFTWARE USED: 
REMARK 200 STARTING MODEL: 
REMARK 200
REMARK 200 REMARK:  

Remark 205, Fiber Diffraction, Fiber Sample Experiment Details

Remark 205 is mandatory if fiber diffraction - non-crystalline sample.

Template

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REMARK 205
REMARK 205 THESE COORDINATES WERE GENERATED FROM FIBER DIFFRACTION
REMARK 205 DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1
REMARK 205 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES OF THESE
REMARK 205 RECORDS ARE MEANINGLESS. 

Remarks 210 and 215, NMR Experiment Details

Remark 210 is mandatory if NMR.

Template

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REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) :
REMARK 210  PH                             :
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      :
REMARK 210  SPECTROMETER FIELD STRENGTH    :
REMARK 210  SPECTROMETER MODEL             :
REMARK 210  SPECTROMETER MANUFACTURER      :
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 :
REMARK 210   METHOD USED                   :
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   :
REMARK 210 CONFORMERS, NUMBER SUBMITTED    :
REMARK 210 CONFORMERS, SELECTION CRITERIA  :
REMARK 210
REMARK 210 REMARK: 

Remark 215 is mandatory if NMR

Template

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REMARK 215                                                              
REMARK 215 NMR STUDY                                                    
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION   
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT        
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON      
REMARK 215 THESE RECORDS ARE MEANINGLESS. 

Remarks 220 and 225, Theoretical Modelling Experiment Details

Remark 220 is mandatory if theoretical model.

Template

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REMARK 220
REMARK 220 EXPERIMENTAL DETAILS
REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING
REMARK 220
REMARK 220 REMARK: 

Remark 225 is mandatory if theoretical model.

Template

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REMARK 225
REMARK 225 THEORETICAL MODEL
REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE.
REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND
REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE
REMARK 225 RECORDS ARE MEANINGLESS.

Remark 230, Neutron Diffraction Experiment Details

Remark 230 is mandatory if neutron diffraction study.

Template

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REMARK 230
REMARK 230 EXPERIMENTAL DETAILS
REMARK 230  EXPERIMENT TYPE                : NEUTRON DIFFRACTION
REMARK 230  DATE OF DATA COLLECTION        :
REMARK 230  TEMPERATURE           (KELVIN) :
REMARK 230  PH                             :
REMARK 230  NUMBER OF CRYSTALS USED        :
REMARK 230
REMARK 230  NEUTRON SOURCE                 :
REMARK 230  BEAMLINE                       :
REMARK 230  WAVELENGTH OR RANGE        (A) :
REMARK 230  MONOCHROMATOR                  :
REMARK 230  OPTICS                         :
REMARK 230
REMARK 230  DETECTOR TYPE                  :
REMARK 230  DETECTOR MANUFACTURER          :
REMARK 230  INTENSITY-INTEGRATION SOFTWARE :
REMARK 230  DATA SCALING SOFTWARE          :
REMARK 230
REMARK 230  NUMBER OF UNIQUE REFLECTIONS   :
REMARK 230  RESOLUTION RANGE HIGH      (A) :
REMARK 230  RESOLUTION RANGE LOW       (A) :
REMARK 230  REJECTION CRITERIA  (SIGMA(I)) :
REMARK 230
REMARK 230 OVERALL.
REMARK 230  COMPLETENESS FOR RANGE     (%) :
REMARK 230  DATA REDUNDANCY                :
REMARK 230  R MERGE                    (I) : 
REMARK 230  R SYM                      (I) : 
REMARK 230  <I/SIGMA(I)> FOR THE DATA SET  :
REMARK 230
REMARK 230 IN THE HIGHEST RESOLUTION SHELL.
REMARK 230  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :
REMARK 230  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) :
REMARK 230  COMPLETENESS FOR SHELL     (%) :
REMARK 230  DATA REDUNDANCY IN SHELL       :
REMARK 230  R MERGE FOR SHELL          (I) : 
REMARK 230  R SYM FOR SHELL            (I) : 
REMARK 230  <I/SIGMA(I)> FOR SHELL         :
REMARK 230
REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE:
REMARK 230 SOFTWARE USED :
REMARK 230 STARTING MODEL:
REMARK 230
REMARK 230 REMARK: 

Remark 240, Electron Diffraction Experiment Details

Remark 240 is mandatory if electron diffraction study.

Template

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REMARK 240
REMARK 240 EXPERIMENTAL DETAILS 
REMARK 240  EXPERIMENT TYPE                : ELECTRON DIFFRACTION
REMARK 240  DATE OF DATA COLLECTION        : 
REMARK 240
REMARK 240 REMARK: 

Remark 250, Other Type of Experiment Details

Remark specific to other kinds of studies, not listed above.
Remark 250 is mandatory if other than x-ray, NMR, theoretical model, neutron, or electron study.

Template

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REMARK 250
REMARK 250 EXPERIMENTAL DETAILS 
REMARK 250  EXPERIMENT TYPE                :
REMARK 250  DATE OF DATA COLLECTION        : 
REMARK 250
REMARK 250 REMARK: 

REMARK 280, Crystal

Remark 280 presents information on the crystal. The solvent content and Matthews coefficient are provided for protein and polypeptide crystals. Crystallization conditions are free text.
Remark 280 is mandatory if single crystal study.

Template

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REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%):
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: FREE TEXT GOES HERE.

REMARK 285, CRYST1

Remark 285 presents information on the unit cell.

Template

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REMARK 285
REMARK 285 CRYST1
REMARK 285 FREE TEXT GOES HERE. 

Example

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REMARK 285                                                            
REMARK 285 CRYST1                                                     
REMARK 285 TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA:  THE DATA WAS      
REMARK 285 COLLECTED ON TWO-DIMENSIONAL CRYSTALS AND HENCE THE        
REMARK 285 C-AXIS REPEAT DOES NOT CORRESPOND TO A REAL REPEAT, BUT    
REMARK 285 INSTEAD REFERS TO THE SAMPLING THAT IS USED TO DESCRIBE    
REMARK 285 THE CONTINUOUS TRANSFORM.  THE C VALUE OF 100.9 IS         
REMARK 285 THEREFORE THE VALUE WHICH SHOULD BE USED IN                
REMARK 285 INTERPRETING THE MEANING OF THE L INDEX. 

REMARK 290, Crystallographic Symmetry

Remark 290 is mandatory for crystalline studies. The remark is generated by PDB.

Template

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REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                  
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21             
REMARK 290                                                            
REMARK 290      SYMOP   SYMMETRY                                      
REMARK 290     NNNMMM   OPERATOR                                      
REMARK 290       1555   X,Y,Z                                         
REMARK 290       2555   1/2-X,-Y,1/2+Z                                
REMARK 290       3555   -X,1/2+Y,1/2-Z                                
REMARK 290       4555   1/2+X,1/2-Y,-Z                                
REMARK 290                                                            
REMARK 290     WHERE NNN -> OPERATOR NUMBER                           
REMARK 290           MMM -> TRANSLATION VECTOR                        
REMARK 290                                                            
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                  
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM   
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY      
REMARK 290 RELATED MOLECULES. 
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000  
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       36.30027  
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       59.50256  
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       59.50256  
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       36.30027  
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000  
REMARK 290                                                            
REMARK 290 REMARK:                                                

Example

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REMARK 290
REMARK 290                                                            
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                  
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21             
REMARK 290                                                            
REMARK 290      SYMOP   SYMMETRY                                      
REMARK 290     NNNMMM   OPERATOR                                      
REMARK 290       1555   X,Y,Z                                         
REMARK 290       2555   1/2-X,-Y,1/2+Z                                
REMARK 290       3555   -X,1/2+Y,1/2-Z                                
REMARK 290       4555   1/2+X,1/2-Y,-Z                                
REMARK 290                                                           
REMARK 290     WHERE NNN -> OPERATOR NUMBER                           
REMARK 290           MMM -> TRANSLATION VECTOR                       
REMARK 290                                                            
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                  
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM   
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY      
REMARK 290 RELATED MOLECULES. 
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000  
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       36.30027  
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       59.50256  
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       59.50256  
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       36.30027 
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000  
REMARK 290                                                            
REMARK 290 REMARK: NULL                                               

REMARK 295, Non-Crystallographic Symmetry

Description of non-crystallographic symmetry. Mandatory when MTRIX records are present.

Template

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REMARK 295
REMARK 295 NON-CRYSTALLOGRAPHIC SYMMETRY
REMARK 295 THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW
REMARK 295 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS
REMARK 295 IN THIS ENTRY.  APPLYING THE APPROPRIATE MTRIX 
REMARK 295 TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD
REMARK 295 APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND.
REMARK 295 CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH
REMARK 295 ATOMS ARE NOT FOUND IN THIS ENTRY.  
REMARK 295
REMARK 295               APPLIED TO          TRANSFORMED TO
REMARK 295   TRANSFORM CHAIN  RESIDUES       CHAIN  RESIDUES     RMSD
REMARK 295     SSS       ?    ? .. ?           ?    ? .. ?       ?
REMARK 295
REMARK 295    WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS
REMARK 295
REMARK 295 REMARK: 

Example

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REMARK 295
REMARK 295 NON-CRYSTALLOGRAPHIC SYMMETRY
REMARK 295 THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW
REMARK 295 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS
REMARK 295 IN THIS ENTRY.  APPLYING THE APPROPRIATE MTRIX 
REMARK 295 TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD
REMARK 295 APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND.
REMARK 295 CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH
REMARK 295 ATOMS ARE NOT FOUND IN THIS ENTRY.  
REMARK 295
REMARK 295               APPLIED TO          TRANSFORMED TO
REMARK 295   TRANSFORM CHAIN  RESIDUES       CHAIN  RESIDUES     RMSD
REMARK 295     SSS
REMARK 295    M  1       A    1 .. 374         C    1 .. 374     0.010
REMARK 295    M  2       B    1 .. 374         D    1 .. 374     0.010
REMARK 295
REMARK 295    WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS
REMARK 295
REMARK 295 REMARK: 

REMARK 300, Biomolecule

Description of the biologically functional molecule (biomolecule) in free text.
Remark 300 is mandatory if Remark 350 is provided.

Template

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REMARK 300
REMARK 300 BIOMOLECULE
REMARK 300 FREE TEXT DESCRIPTION OF THE BIOLOGICALLY FUNCTIONAL 
REMARK 300 MOLECULE.

Example

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REMARK 300
REMARK 300 BIOMOLECULE
REMARK 300 THE CATALYTIC SUBUNIT OF LIVER ALCOHOL DEHYDROGENASE FROM
REMARK 300 EQUUS CABALLUS IS A HOMO DIMER. 

REMARK 350, Generating the Biomolecule

Remark 350 presents all transformations, both crystallographic and non-crystallographic, needed to generate the biomolecule. These transformations operate on the coordinates in the entry.
Remark 350 is mandatory if Remark 300 is provided.

Template

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REMARK 350  
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN 
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND 
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. 
REMARK 350
REMARK 350 APPLY THE FOLLOWING TO CHAINS: ?, ?...
REMARK 350   BIOMT1   N  N.NNNNNN  N.NNNNNN  N.NNNNNN        N.NNNNN
REMARK 350   BIOMT2   N  N.NNNNNN  N.NNNNNN  N.NNNNNN        N.NNNNN
REMARK 350   BIOMT3   N  N.NNNNNN  N.NNNNNN  N.NNNNNN        N.NNNNN 

Example

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REMARK 350  
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN 
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND 
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. 
REMARK 350
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000       60.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000     -120.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F
REMARK 350   BIOMT1   3  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   3  0.000000 -1.000000  0.000000       60.00000
REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   4 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   4  0.000000 -1.000000  0.000000     -120.00000
REMARK 350   BIOMT3   4  0.000000  0.000000  1.000000        0.00000

REMARK 350  
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN 
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND 
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. 
REMARK 350
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H
REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J, K, L
REMARK 350   BIOMT1   1 -0.500000 -0.865983  0.000000        0.00000
REMARK 350   BIOMT2   1  0.866068 -0.500000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000

REMARK 375, Special Position

Remark 375 specifies atoms that are known to lie in particular locations, related by the symmetry elements, at which objects may be placed if and only if they possess symmetry which coincides with that of the cell.

Template

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REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 FREE TEXT GOES HERE. 

Example

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REMARK 375                                                            
REMARK 375 SPECIAL POSITION                                           
REMARK 375      HOH   301  LIES ON A SPECIAL POSITION.                 
REMARK 375      HOH    77  LIES ON A SPECIAL POSITION.                 

REMARK 375                                                         
REMARK 375 SPECIAL POSITION                                        
REMARK 375 MG   MO4 A  10  LIES ON A SPECIAL POSITION.              
REMARK 375      HOH A  13  LIES ON A SPECIAL POSITION.              
REMARK 375      HOH A  28  LIES ON A SPECIAL POSITION.              
REMARK 375      HOH A  36  LIES ON A SPECIAL POSITION.              

REMARK 400, Compound

Further details on the macromolecular contents of the entry.

Template

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REMARK 400
REMARK 400 COMPOUND
REMARK 400 FREE TEXT GOES HERE.

REMARK 450, Source

Further details on the biological source of the macromolecular contents of the entry.

Template

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REMARK 450
REMARK 450 SOURCE
REMARK 450 FREE TEXT GOES HERE.

REMARK 460, Non-IUPAC Names

Remark 460 is mandatory when IUPAC-IUB rules are not strictly followed in naming side-chain atoms.

Template

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REMARK 460
REMARK 460 NON-IUPAC
REMARK 460 BY REQUEST OF THE DEPOSITOR, THE PROTEIN DATA BANK HAS NOT
REMARK 460 APPLIED THE IUPAC-IUB RECOMMENDATIONS REGARDING THE
REMARK 460 DESIGNATION OF BRANCHES 1 AND 2 OF SIDE-CHAIN ATOMS IN
REMARK 460 RESIDUES ARG, ASP, GLU, LEU, PHE, TYR, AND VAL TO THIS
REMARK 460 ENTRY. 

REMARK 470, Missing Atom

Non-hydrogen atoms of standard residues which are missing from the coordinates are listed. Missing HETATMS are not listed here.

Template

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REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;  
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; 
REMARK 470 I=INSERTION CODE):                                          
REMARK 470   M RES CSSEQI  ATOMS                                       

Example

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REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;  
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; 
REMARK 470 I=INSERTION CODE):                                          
REMARK 470   M RES CSSEQI  ATOMS                                       
REMARK 470     ARG A 412    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     ARG A 456    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     GLU A 486    CG   CD   OE1  OE2                         
REMARK 470     GLU A 547    CG   CD   OE1  OE2                         
REMARK 470     GLU A 548    CG   CD   OE1  OE2                         
REMARK 470     LYS A 606    CG   CD   CE   NZ                          
REMARK 470     ARG B 456    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     ASP B 484    CG   OD1  OD2                              
REMARK 470     GLN B 485    CG   CD   OE1  NE2                         
REMARK 470     GLU B 486    CG   CD   OE1  OE2                         
REMARK 470     ARG B 490    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     GLU B 522    CG   CD   OE1  OE2                         
REMARK 470     ARG B 576    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     ASP B 599    CG   OD1  OD2

REMARK 500, Geometry and Stereochemistry

Further details on the stereochemistry of the structure. This remark is generated by PDB, but may also be provided by the depositor. Additional subtopics may be added as needed.

Template

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY 
REMARK 500 SUBTOPIC: 
REMARK 500 
REMARK 500 FREE TEXT GOES HERE.

Example, close contacts

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC 
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  SOME OF THESE MAY BE ATOMS
REMARK 500 LOCATED ON SPECIAL POSITIONS IN THE CELL.
REMARK 500
REMARK 500 DISTANCE CUTOFF: 2.2 ANGSTROMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   CB   LEU D    68  -  CE   LYS E    76     1656     2.10
REMARK 500   CB   THR D   173  -  O    HOH    1151     4455     1.73
REMARK 500   O    HOH    1151  -  CB   THR D   173     4566     1.73
REMARK 500   CZ   ARG D    64  -  O    HOH    1422     3656     1.75 

REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   O    HOH     761  -  O    ARG      17              1.89
REMARK 500   O    HOH     806  -  N    ARG      88              1.46

Example, non-CIS, non-trans

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500                                 MODEL     OMEGA
REMARK 500 VAL A  123    GLN A  124          0       221.48
REMARK 500 VAL B  123    GLN B  124          0       222.43

Example, chiral centers

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE: 
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,A12)
REMARK 500
REMARK 500  M RES CSSEQI
REMARK 500  0 GLU     1       ALPHA-CARBON
REMARK 500  0 GLU     1       SIDE-CHAIN
REMARK 500  0 GLU     1       ALPHA-CARBON

Example, covalent bond angles

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 4*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(2X,A4,17X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500  0 ASP     3   C-1 -  N   -  CA  ANGL. DEV. =  21.7 DEGREES

Example, torsion angles

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES 
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; 
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE: 
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500  0 VAL    26     -174.85   -134.80
REMARK 500  0 MET    61       46.11   -176.53

REMARK 525, Solvent

Remarks specific to the solvent molecules of the entry.

Template

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REMARK 525
REMARK 525 SOLVENT
REMARK 525 FREE TEXT GOES HERE. 

Example

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REMARK 525
REMARK 525 SOLVENT
REMARK 525 MANY OF THE WATER MOLECULES APPEAR TO BE ASSOCIATED WITH
REMARK 525 A SYMMETRY-RELATED MOLECULE. 

REMARK 525
REMARK 525 SOLVENT
REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED
REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE
REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL
REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525 
REMARK 525  M RES CSSEQI                                            
REMARK 525  0 HOH    561      DISTANCE =  5.07 ANGSTROMS            
REMARK 525  0 HOH    791      DISTANCE =  5.08 ANGSTROMS

REMARK 550, SEGID

Description of the segment identifiers used in ATOM/HETATM.

Template

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REMARK 550
REMARK 550 SEGID
REMARK 550 FREE TEXT GOES HERE.

Example

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REMARK 550
REMARK 550 SEGID
REMARK 550 RESIDUES 1-55, SEGID VH1 ARE THE HEAVY CHAIN, VARIABLE 
REMARK 550 REGION 1.  RESIDUES 56-100, SEGID VH2 ARE THE HEAVY CHAIN, 
REMARK 550 VARIABLE REGION 2,AND RESIDUES 101-150., SEGID VH3 ARE THE 
REMARK 550 HEAVY CHAIN.

REMARK 600, Heterogen

Further details on the heterogens in the entry.

Template

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REMARK 600
REMARK 600 HETEROGEN
REMARK 600 FREE TEXT GOES HERE.

Example

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REMARK 600                                                            
REMARK 600 HETEROGEN                                                  
REMARK 600 HET GROUP TRIVIAL NAME: PHOSPHOTYROSINE                    
REMARK 600 EMPIRICAL FORMULA     : C9 O6 N P                          
REMARK 600                                                            
REMARK 600                O                                           
REMARK 600               /                           _                
REMARK 600          O = C           C = C           O                 
REMARK 600               \         /     \         /   _              
REMARK 600                C - C - C       C - O - P - O               
REMARK 600               /         \\   //        \\                  
REMARK 600              N           C - C           O                 
REMARK 600                                                            
REMARK 600                                                            
REMARK 600 NUMBER OF ATOMS IN GROUP: 17 (EXCLUDING HYDROGENS) 

REMARK 650, Helix

Further details on the helix contents of the entry.

Template

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REMARK 650
REMARK 650 HELIX
REMARK 650 FREE TEXT GOES HERE.

Example

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REMARK 650                                                            
REMARK 650 HELIX                                                      
REMARK 650 DETERMINATION METHOD: KDSSP                                
REMARK 650 THE MAJOR DOMAINS ARE: "N" FOR N-TERMINAL DOMAIN, "B" FOR  
REMARK 650 BETA-BARREL DOMAIN, AND "C" FOR C-TERMINAL DOMAIN. "F"     
REMARK 650 REFERS TO THE ACTIVE SITE FLAP.  ALPHA HELICES ARE NAMED   
REMARK 650 WITH TWO CHARACTERS, THE FIRST REFERRING TO THE DOMAIN     
REMARK 650 IN WHICH THEY OCCUR. 

REMARK 700, Sheet

Further details on the sheet contents of the structure. Several standard templates are included here.

Template

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REMARK 700
REMARK 700 SHEET
REMARK 700 FREE TEXT GOES HERE. 

REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD:                                 
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED.  IN
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, 
REMARK 700 TWO SHEETS ARE DEFINED.  STRANDS N1, N2, N3 AND N4 OF SHEET
REMARK 700 XXX AND XXX ARE IDENTICAL. 

REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD:                                 
REMARK 700 THE SHEET PRESENTED AS XXX ON SHEET RECORDS BELOW IS
REMARK 700 ACTUALLY AN N-STRANDED BETA-BARREL.  THIS IS
REMARK 700 REPRESENTED BY A N+1-STRANDED SHEET IN WHICH THE FIRST AND
REMARK 700 LAST STRANDS ARE IDENTICAL. 

REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD:                                 
REMARK 700 THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. 
REMARK 700 EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE
REMARK 700 IDENTICAL STRANDS. 
REMARK 700 SHEETS XXX AND XXX REPRESENT ONE BIFURCATED SHEET. 
REMARK 700 SHEETS XXX AND XXX REPRESENT ONE BIFURCATED SHEET. 

N1, N2, N3 and N4 represent strand numbers, and XXX represents sheet identifiers.

When the remark for several bifurcated sheets is used, its last line is repeated for the appropriate number of bifurcated sheets, as shown in the last template above.

Example

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REMARK 700
REMARK 700 SHEET
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED.  IN   
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
REMARK 700 TWO SHEETS are defined.  STRANDS 3, 4, AND 5 
REMARK 700 OF SHEET *B2A* AND *B2B* ARE IDENTICAL.  STRANDS 3, 4, AND
REMARK 700 5 OF SHEET *B2C* AND *B2D* ARE IDENTICAL.                 

REMARK 700                                                           
REMARK 700 SHEET
REMARK 700 STRANDS 1 TO 4 OF THE BETA-SHEET HAVE GREEK-KEY TOPOLOGY. 
REMARK 700 THE SHEET FORMS A FIVE-STRANDED BETA-BARREL WITH BULGES IN 
REMARK 700 STRANDS 3 AND 5.  IN ORDER TO REPRESENT THIS FEATURE IN THE
REMARK 700 SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.               

REMARK 700                                                            
REMARK 700 SHEET                                                      
REMARK 700 THE SHEET PRESENTED AS S5 ON SHEET RECORDS BELOW IS        
REMARK 700 ACTUALLY A 6-STRANDED BETA-BARREL.  THIS IS                
REMARK 700 REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND   
REMARK 700 LAST STRANDS ARE IDENTICAL.                                

REMARK 750, Turn

Further details on the turns.

Template

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REMARK 750
REMARK 750 TURN
REMARK 750 FREE TEXT GOES HERE.

Example

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REMARK 750
REMARK 750 TURN
REMARK 750  TURN_ID: T4, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES    
REMARK 750  DEVIATE BY MORE THAN PLUS,MINUS 45 DEGREES FROM THE IDEAL  
REMARK 750  VALUES USED BY WILMOT & THORNTON(1989)). 
REMARK 750                                                             
REMARK 750  TURN_ID: T10, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES   
REMARK 750  DEVIATE BY MORE THAN PLUS,MINUS 45 DEGREES FROM THE IDEAL  
REMARK 750  VALUES USED BY WILMOT & THORNTON(1989)). 
REMARK 750                                                             
REMARK 750  TURN_ID: T16, TYPE VIII (ONE OR MORE OF THE PHI, PSI       
REMARK 750  ANGLES DEVIATE BY MORE THAN PLUS,MINUS 45 DEGREES FROM     
REMARK 750  THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). 

REMARK 800, Site

Further details on the site contents of the entry.
Remark 800 is mandatory if site records exist.

Template

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REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: FREE TEXT GOES HERE. 
REMARK 800 SITE_DESCRIPTION: FREE TEXT GOES HERE.

Example

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REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: RCA
REMARK 800 SITE_DESCRIPTION: DESIGNATED RECOGNITION REGION IN PRIMARY
REMARK 800 REFERENCE.  PROPOSED TO AFFECT SUBSTRATE SPECIFICITY.      
REMARK 800
REMARK 800 SITE_IDENTIFIER: RCB                                       
REMARK 800 SITE_DESCRIPTION: DESIGNATED RECOGNITION REGION IN PRIMARY 
REMARK 800  REFERENCE.  PROPOSED TO AFFECT SUBSTRATE SPECIFICITY.     
 

REMARK 850, Revisions to Deposited Coordinates, Before Release

Template

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REMARK 850
REMARK 850 CORRECTION BEFORE RELEASE
REMARK 850 ORIGINAL DEPOSITION REVISED PRIOR TO RELEASE
REMARK 850 DATE REVISED: DD-MMM-YYYY  TRACKING NUMBER: T?

DD is a number 01 through 31, MMM is a 3 letter abbreviation for the month, and YYYY is the year.

Example

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REMARK 850                                                         
REMARK 850 CORRECTION BEFORE RELEASE                               
REMARK 850 ORIGINAL DEPOSITION REVISED PRIOR TO RELEASE            
REMARK 850 DATE REVISED: 13-FEB-1996  TRACKING NUMBER: T7770       
REMARK 850 DATE REVISED: 10-APR-1996  TRACKING NUMBER: T8125       

REMARK 860, Correction, After Release

Further details on corrections that have been made to the PDB entry, as referred to in the REVDAT record.

Template

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 860
REMARK 860 CORRECTION AFTER RELEASE
REMARK 860 FREE TEXT GOES HERE. 

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 860
REMARK 860 CORRECTION
REMARK 860 CORRECT RESIDUE IDENTIFICATION ON SITE RECORDS.  ADD       
REMARK 860 RESIDUE TO SITE RECORDS.  15-JUL-81.                       
REMARK 860                                                            
REMARK 860 CORRECT DATES IN REMARKS 7 AND 16. 15-JAN-82.    
REMARK 860                                                            
REMARK 860 CORRECT ATOM NAME FOR ATOM 6 FROM CG2 TO CG1.  07-MAR-83.  
REMARK 860                                                            
REMARK 860 CHANGE RESIDUE 122 FROM ASN TO ASP.  ADD REFERENCE.        
REMARK 860  12-MAY-83.                                      
REMARK 860                                                            
REMARK 860 INSERT REVDAT RECORDS. 30-SEP-83.              
REMARK 860                                                            
REMARK 860 CORRECT CODEN FOR REFERENCE 1.  27-OCT-83.     

REMARK 900, Related Entries

This remark gives ID codes of PDB files related to the entry. These may include coordinate entries deposited as a related set, the structure factor or NMR restraint file related to the entry, or the file containing the biologically functional molecule ("biomolecule") generated by the PDB from symmetry records.

Template

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 900 
REMARK 900 RELATED ENTRIES
REMARK 900 FREE TEXT GOES HERE.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 THE BIOMOLECULE RELATED TO THIS ENTRY HAS BEEN GENERATED
REMARK 900 AND IS AVAILABLE AS PDB FILE BIO1ABC.PDB

REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 THE STRUCTURE FACTORS FOR THIS EXPERIMENT ARE AVAILABLE AS
REMARK 900 PDB FILE R1ABCSF.ENT

REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 THE LIST OF EXPERIMENTAL RESTRAINTS IS AVAILABLE AS PDB
REMARK 900 FILE 1ABC.MR

REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 THE BIOMOLECULE IS AVAILABLE AS PDB FILE BIO1ABC.PDB

REMARK 999 Sequence

Further details on the sequence.

For cases where there are gaps in the structure as reflected in missing ATOM records missing N-terminus and C-terminus residues are delineated in REMARK 999 records, whereas internal structural gaps are represented in SEQADV records. Several cases must be considered when evaluating these REMARK 999 records:

1. The missing N-terminus atoms are not found in the ATOM record as they represent precursor sequence and are not found in the mature protein.
2. The missing N-terminus residues were not found in the density map. Although PDB will attempt to flag these as SEQADV records, we cannot guarantee that they will always be handled uniformly. The primary reason for this inconsistency is that in a number of cases, neither PDB nor the depositors, are certain where chains start and end.

Template

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 FREE TEXT GOES HERE.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 999                                                            
REMARK 999 SEQUENCE                                                   
REMARK 999 1ARL       SWS     P00730       1 -   110 NOT IN ATOMS LIST
REMARK 999 1ARL       SWS     P00730     418 -   419 NOT IN ATOMS LIST
REMARK 999                                                            
REMARK 999  REFERENCE                                                 
REMARK 999   REFERENCE: PETRA, ET AL., (1971) BIOCHEMISTRY 10, PP     
REMARK 999   4023-4025.                                               
REMARK 999                                                            
REMARK 999   SHOHAM, G., NECHUSHTAI, R., STEPPUN, J.,NELSON, H.,      
REMARK 999   NELSON N., UNPUBLISHED RESULTS.                          
REMARK 999                                                            
REMARK 999   LE HUEROU,I., GUILLOTEAU P., TOULLEC, R., PUIGSERVER, A.,
REMARK 999   WICKER,C., (1991) BIOCHEMICAL, BIOPHYSICAL RESEARCH      
REMARK 999   COMM., 175, PP 110 - 116.                                
REMARK 999                                                            
REMARK 999 THE SEQUENCE USED IS THAT PROVIDED BY THE CDNA, WHICH      
REMARK 999 CORRECTS SEVERAL ASP/ASN AND GLU/GLN MISASSIGNMENTS.       

REMARK 999                                                            
REMARK 999 SEQUENCE                                                   
REMARK 999 MET A    1  - MET A    1  - MISSING FROM SWS    P10599     
REMARK 999 1CQG  B    SWS     P27695       1 -    57 NOT IN ATOMS LIST
REMARK 999 1CQG  B    SWS     P27695      71 -   317 NOT IN ATOMS LIST
REMARK 999                                                            
REMARK 999 THR AT POSITION 74 WAS FOUND BY WOLMAN ET AL., JOURNAL OF  
REMARK 999 BIOCHEMISTRY 263, 15506 (1988).                            


3. Primary Structure Section

The primary structure section of a PDB file contains the sequence of residues in each chain of the macromolecule. Embedded in these records are chain identifiers and sequence numbers that allow other records to link into the sequence.


DBREF

Overview

The DBREF record provides cross-reference links between PDB sequences and the corresponding database entry or entries. A cross reference to the sequence database is mandatory for each peptide chain with a length greater than ten (10) residues. For nucleic acid entries a DBREF record pointing to the Nucleic Acid Database (NDB) is mandatory when the corresponding entry exists in NDB.

Record Format

COLUMNS       DATA TYPE       FIELD          DEFINITION                            
--------------------------------------------------------------------------------
 1 -  6       Record name     "DBREF "                                          
 8 - 11       IDcode          idCode         ID code of this entry.             
13            Character       chainID        Chain identifier.                  
15 - 18       Integer         seqBegin       Initial sequence number of the PDB 
                                             sequence segment.                  
19            AChar           insertBegin    Initial insertion code of the PDB  
                                             sequence segment.                  
21 - 24       Integer         seqEnd         Ending sequence number of the PDB  
                                             sequence segment.                  
25            AChar           insertEnd      Ending insertion code of the PDB   
                                             sequence segment.                  
27 - 32       LString         database       Sequence database name.  "PDB" when
                                             a corresponding sequence database  
                                             entry has not been identified.     
34 - 41       LString         dbAccession    Sequence database accession code.  
                                             For GenBank entries, this is the   
                                             NCBI gi number.                    
43 - 54       LString         dbIdCode       Sequence database identification   
                                             code.  For GenBank entries, this is
                                             the accession code.                
56 - 60       Integer         dbseqBegin     Initial sequence number of the     
                                             database seqment.                  
61            AChar           idbnsBeg       Insertion code of initial residue  
                                             of the segment, if PDB is the      
                                             reference.                         
63 - 67       Integer         dbseqEnd       Ending sequence number of the      
                                             database segment.                  
68            AChar           dbinsEnd       Insertion code of the ending       
                                             residue of the segment, if PDB is  
                                             the reference.

Details

* PDB entries contain multi-chain molecules with sequences that may be wild type, variant, or synthetic. Sequences may also have been modified through site-directed mutagenesis experiments (engineered). A number of PDB entries report structures of domains cleaved from larger molecules.

* The DBREF record was designed to account for these differences by providing explicit correlations between contiguous segments of sequences as given in the PDB ATOM records and the sequence database entry. Several cases are easily represented by means of pointers between the databases using DBREF. PDB entries containing heteropolymers are linked to different sequence database entries. In some cases, such as those PDB entries containing immunoglobulin Fab fragments, each chain is linked to two different SWISS-PROT, PIR, and/or GenBank entries. This facility is needed because these databases represent sequences for the various immunoglobulin domains as separate entries. DBREF also is able to represent molecules engineered by altering the gene (fusing genes, altering sequences, creating chimeras, or circularly permuting sequences). This design has the additional advantage that it will be possible to construct pointers to other relevant databases such as the Nucleic Acid Database, BioMagResBank, and databases describing sequence motifs (e.g., PROSITE, BLOCKS).

* Database names and their abbreviations as used on DBREF records.

   Database name                            database (code in columns 27 - 32)
   ---------------------------------------------------------------------------
   BioMagResBank                            BMRB
   BLOCKS                                   BLOCKS
   European Molecular Biology Laboratory    EMBL
   GenBank                                  GB
   Genome Data Base                         GDB
   Nucleic Acid Database                    NDB
   PROSITE                                  PROSIT
   Protein Data Bank                        PDB
   Protein Identification Resource          PIR
   SWISS-PROT                               SWS
   TREMBL                                   TREMBL

* When no sequence numbers are given (columns 15 - 25 and 56 - 68), then the mapping is between database entries rather than segments within an entry. For example, this is normally used to point to the related NDB entry.

* DBREF records present sequence correlations between PDB ATOM records and corresponding PIR, GenBank, or SWISS-PROT, etc. entries.

* PDB does not guarantee that all possible references to the listed databases will be provided. In most cases, only one reference to a sequence database will be provided.

* PDB entries containing chains for which residues are missing primarily due to disorder contain several DBREF records, each linking an observed sequence segment to a sequence database entry.

* If no reference is found in the sequence databases, then the PDB entry itself is given as the reference.

* For nucleic acid entries a DBREF record pointing to the Nucleic Acid Database (NDB) is mandatory when the corresponding entry exists in NDB.

* Selection of the appropriate sequence database entry or entries to be linked to a PDB entry is done on the basis of the sequence and its biological source. Questions on entry assignment that may arise are resolved by consultation with database staff.

Verification/Validation/Value Authority Control

The sequence database entry found during PDB's search is compared to that provided by the depositor and any differences are resolved or annotated.

In most cases, only one reference to a sequence database will be provided. PDB does not guarantee that all possible references to the listed databases will be provided.

Relationships to Other Record Types

DBREF represents the sequence as found in ATOM and HETATM records.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
DBREF  1ABC B    1B   36  PDB    1ABC     1ABC             1B    36
DBREF  3AKY      3   220  SWS    P07170   KAD1_YEAST       5    222 
DBREF  1HAN      2   288  GB     397884   X66122           1    287 
DBREF  3HSV A    1    92  SWS    P22121   HSF_KLULA      193    284
DBREF  3HSV B    1    92  SWS    P22121   HSF_KLULA      193    284
DBREF  1ARL      1   307  SWS    P00730   CBPA_BOVIN     111    417  
DBREF  249D A    1    12  NDB    BDL070   BDL070           1     12   
DBREF  249D B   13    24  NDB    BDL070   BDL070          13     24   
DBREF  249D C   26    36  NDB    BDL070   BDL070          26     36   
DBREF  249D D   37    48  NDB    BDL070   BDL070          37     48   


SEQADV

Overview

The SEQADV record identifies conflicts between sequence information in the ATOM records of the PDB entry and the sequence database entry given on DBREF. Please note that these records were designed to identify differences and not errors. No assumption is made as to which database contains the correct data. PDB may include REMARK records in the entry that reflect the depositor's view of which database has the correct sequence.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                          
----------------------------------------------------------------------------------
 1 -  6        Record name     "SEQADV"                                           
 8 - 11        IDcode          idCode         ID code of this entry.              
13 - 15        Residue name    resName        Name of the PDB residue in conflict.
17             Character       chainID        PDB chain identifier.               
19 - 22        Integer         seqNum         PDB sequence number.                
23             AChar           iCode          PDB insertion code.                 
25 - 28        LString         database       Sequence database name.             
30 - 38        LString         dbIdCode       Sequence database accession     
                                              number.                             
40 - 42        Residue name    dbRes          Sequence database residue name.     
44 - 48        Integer         dbSeq          Sequence database sequence number.  
50 - 70        LString         conflict       Conflict comment.                

Details

* For cases where there are gaps in the structure as reflected in missing ATOM records, SEQADV records are produced which reflect the lack of correlation between the chain and the sequence database entry. (Several DBREF records are also produced.) Note that internal structural gaps are represented in SEQADV records, whereas missing N-terminus and C-terminus residues are delineated in REMARK 999 records

* If the missing N-terminus residues were not found in the density map, the PDB will attempt to flag these as SEQADV records. However, we cannot guarantee that they will always be handled uniformly since, in a number of cases, neither PDB nor the depositors are certain where chains start and end.

* In a number of cases, conflicts between the sequences found in PDB entries and in PIR or SWISS-PROT entries have been noted. There are several possible reasons for these conflicts, including natural variants or engineered sequences (mutants), polymorphic sequences, or ambiguous or conflicting experimental results. These discrepancies, which were previously described in REMARK records, are now reported in SEQADV.

* SEQADV describes conflicts between residue sequences given by PDB ATOM/HETATM records and those in the appropriate sequence database entry, such as residues missing due to disorder.

* This record will give a description of the differences between the sequence database entries and complete chains. If a chain is referenced by more than one sequence database entry, as in the case of fused genes, then SEQADV will describe the relationship between each chain segment.

* Some of the possible conflict comments:

Cloning artifact
Conflict
Engineered
Disordered
Gap in PDB entry
Missing from [database name]
Variant
Insertion
Deletion
Microheterogeneity
D-configuration

* When conflicts arise which are not classifiable by these terms, a reference to either a published paper, a PDB entry, or a REMARK within the entry is given. References are given in the form YY-VOL-PAGE-CODEN where YY is year of publication, VOL is the journal volume number, PAGE is the starting page and CODEN is the 4-digit code assigned to journals by PDB and the Cambridge Crystallographic Data Centre (CCDC).

* When reference is made to a PDB entry, then the form is PDB: 1ABC, where 1ABC is the relevant entry ID code.

* Finally, the comment "SEE REMARK 999" is included when the explanation for the conflict is too long to fit the SEQADV record.

* Microheterogeneity is to be represented as a variant with one of the possible residues in the site being selected (arbitrarily) as the primary residue, in which case a SEQADV record must be provided for the alternate residue.

Verification/Validation/Value Authority Control

SEQADV records are automatically generated by the PDB.

Relationships to Other Record Types

SEQADV refers to the sequence as found in the ATOM and HETATM records, and to the sequence database reference found on DBREF.

REMARK 999 contains text explaining discrepancies when the explanation is too lengthy to fit in SEQADV.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SEQADV 1ABC ASN A  100A SWS  P10725    ASP   100 1994-300-1200-0070
SEQADV 2ABC ASN A  100A SWS  P10725    ASP   100 PDB: 1ABC
SEQADV 3ABC MET A   -1  SWS  P10725              CLONING ARTIFACT
SEQADV 3ABC GLY A   50  SWS  P10725    VAL    50 ENGINEERED


SEQRES

Overview

SEQRES records contain the amino acid or nucleic acid sequence of residues in each chain of the macromolecule that was studied.

Record Format

COLUMNS        DATA TYPE       FIELD         DEFINITION                           
---------------------------------------------------------------------------------
 1 -  6        Record name     "SEQRES"                                           
 9 - 10        Integer         serNum        Serial number of the SEQRES record   
                                             for the current chain.  Starts at 1  
                                             and increments by one each line.     
                                             Reset to 1 for each chain.           
12             Character       chainID       Chain identifier.  This may be any   
                                             single legal character, including a  
                                             blank which is used if there is      
                                             only one chain.                      
14 - 17        Integer         numRes        Number of residues in the chain.     
                                             This value is repeated on every      
                                             record.                              
20 - 22        Residue name    resName       Residue name.                        
24 - 26        Residue name    resName       Residue name.                        
28 - 30        Residue name    resName       Residue name.                        
32 - 34        Residue name    resName       Residue name.                        
36 - 38        Residue name    resName       Residue name.                        
40 - 42        Residue name    resName       Residue name.                        
44 - 46        Residue name    resName       Residue name.                        
48 - 50        Residue name    resName       Residue name.                        
52 - 54        Residue name    resName       Residue name.                        
56 - 58        Residue name    resName       Residue name.                        
60 - 62        Residue name    resName       Residue name.                        
64 - 66        Residue name    resName       Residue name.                        
68 - 70        Residue name    resName       Residue name.                        

Details

* PDB entries use the three-letter abbreviation for amino acid names and the one letter code for nucleic acids.

* In the case of non-standard groups, a hetID of up to three (3) alphanumeric characters is used. Common HET names appear in the HET dictionary.

* Each covalently contiguous sequence of residues (connected via the "backbone" atoms) is represented as an individual chain.

* Heterogens which are integrated into the backbone of the chain are listed as being part of the chain and are included in the SEQRES records for that chain.

* Each set of SEQRES records and each HET group is assigned a component number. The component number is assigned serially beginning with 1 for the first set of SEQRES records. This number is given explicitly in the FORMUL record, but only implicitly in the SEQRES record.

* The SEQRES records must list residues present in the molecule studied, even if the coordinates are not present.

* C- and N-terminus residues for which no coordinates are provided due to disorder must be listed on SEQRES.

* All occurrences of standard amino or nucleic acid residues (ATOM records) must be listed on a SEQRES record. This implies that a numRes of 1 is valid.

* No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U, I).

* If the entire residue sequence is unknown, the serNum in column 10 is "0", the number of residues thought to comprise the molecule is entered as numRes in columns 14 - 17, and resName in columns 20 - 22 is "UNK".

* In case of microheterogeneity, only one of the sequences is presented. A REMARK is generated to explain this and a SEQADV is also generated.

Verification/Validation/Value Authority Control

The residues presented on the SEQRES records must agree with those found in the ATOM records.

The SEQRES records are checked by PDB using the sequence databases and information provided by the depositor.

SEQRES is compared to the ATOM records during processing, and both are checked against the sequence database. All discrepancies are either resolved or annotated in the entry.

Relationships to Other Record Types

The residues presented on the SEQRES records must agree with those found in the ATOM records. DBREF refers to the corresponding entry in the sequence databases. SEQADV lists all discrepancies between the entry's sequence for which there are coordinates and that referenced in the sequence database. MODRES describes modifications to a standard residue.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SEQRES   1 A   21  GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU
SEQRES   2 A   21  TYR GLN LEU GLU ASN TYR CYS ASN                    
SEQRES   1 B   30  PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU
SEQRES   2 B   30  ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR
SEQRES   3 B   30  THR PRO LYS ALA                                    
SEQRES   1 C   21  GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU
SEQRES   2 C   21  TYR GLN LEU GLU ASN TYR CYS ASN                    
SEQRES   1 D   30  PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU
SEQRES   2 D   30  ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR
SEQRES   3 D   30  THR PRO LYS ALA                                    

Known Problems

Polysaccharides do not lend themselves to being represented in SEQRES.

There is no mechanism provided to describe sequence runs when the exact ordering of the sequence is not known.

For cyclic peptides, PDB arbitrarily assigns a residue as the N-terminus.

For microheterogeneity only one of the possible residues in a given position is provided in SEQRES.

No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U).


MODRES

Overview

The MODRES record provides descriptions of modifications (e.g., chemical or post-translational) to protein and nucleic acid residues. Included are a mapping between residue names given in a PDB entry and standard residues.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
--------------------------------------------------------------------------------
 1 -  6        Record name     "MODRES"                                          
 8 - 11        IDcode          idCode         ID code of this entry.             
13 - 15        Residue name    resName        Residue name used in this entry.   
17             Character       chainID        Chain identifier.                  
19 - 22        Integer         seqNum         Sequence number.                   
23             AChar           iCode          Insertion code.                    
25 - 27        Residue name    stdRes         Standard residue name.             
30 - 70        String          comment        Description of the residue         
                                              modification.                      

Details

* Residues modified post-translationally, enzymatically, or by design are described in MODRES records. In those cases where PDB has opted to use a non-standard residue name for the residue, MODRES also provides a mapping to the precursor standard residue name.

* MODRES is mandatory for when modified standard residues exist in the entry.

* Examples of some modification descriptions:

Glycosylation site
Post-translational modification
Designed chemical modification
Phosphorylation site
Blocked N-terminus
Aminated C-terminus
D-configuration
Reduced peptide bond

* MODRES is not required if coordinate records are not provided for the modified residue.

* D-amino acids are given their own resName , i.e., DAL for D-alanine. This resName appears in the SEQRES records, and has the associated SEQADV, MODRES, HET, and FORMUL records. The coordinates are given as HETATMs within the ATOM records and occur in the correct order within the chain. This ordering is an exception to the stated Order of Records.

* When a standard residue name is used to describe a modified site, resName (columns 13-15) and stdRES (columns 25-27) contain the same value.

Verification/Validation/Value Authority Control

MODRES is generated by the PDB.

Relationships to Other Record Types

MODRES maps ATOM and HETATM records to the standard residue names. SEQADV, HET, and FORMUL may also appear.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
MODRES 1ABC ASN A   22A ASN  GLYCOSYLATION SITE
MODRES 2ABC TTQ A   50A TRP  POST-TRANSLATIONAL MODIFICATION
MODRES 3ABC DAL A   32  ALA  POST-TRANSLATIONAL MODIFICATION,D-ALANINE
MODRES 3ABC DAL B   32  ALA  POST-TRANSLATIONAL MODIFICATION,D-ALANINE

Known Problems

Mapping between SEQRES and MODRES residue numbers when the numbering is non-sequential has to be constructed using DBREF, SEQRES, and SEQADV.


4. Heterogen Section

The heterogen section of a PDB file contains the complete description of non-standard residues in the entry.


HET

Overview

HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are:

- not one of the standard amino acids, and
- not one of the nucleic acids (C, G, A, T, U, and I), and
- not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and
- not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name.

Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK.

Record Format

COLUMNS        DATA TYPE       FIELD         DEFINITION                          
---------------------------------------------------------------------------------
 1 -  6        Record name     "HET   "                                          
 8 - 10        LString(3)      hetID         Het identifier, right-justified.    
13             Character       ChainID       Chain identifier.                   
14 - 17        Integer         seqNum        Sequence number.                    
18             AChar           iCode         Insertion code.                     
21 - 25        Integer         numHetAtoms   Number of HETATM records for the    
                                             group present in the entry.         
31 - 70        String          text          Text describing Het group.          

Details

* Each HET group is assigned a hetID of not more than three (3) alphanumeric characters. The sequence number, chain identifier, insertion code, and number of coordinate records are given for each occurrence of the HET group in the entry. The chemical name of the HET group is given in the HETNAM record and synonyms for the chemical name are given in the HETSYN records.

* There is a separate HET record for each occurrence of the HET group in an entry.

* A particular HET group is represented in the PDB archives with a unique hetID.

* PDB entries do not have HET records for water molecules.

* The Text field is for descriptive material. The token PART_OF followed by a value may be used to indicate that the HET group is part of a larger group which has been represented by its separate components (e.g., PART_OF: actinomycin). Segment identifiers, columns 73 - 76 of ATOM/HETATM records, may also be used to relate individual components of a large HET group.

* Unknown atoms or ions will be represented as UNX with the chemical formula X1.

Verification/Validation/Value Authority Control

For each het group that appears in the entry, PDB checks that the corresponding HET, HETNAM, HETSYN, FORMUL, HETATM, and CONECT records appear, if applicable. The HET record is generated automatically by PDB using the het group dictionary and information from the HETATM records.

Each unique hetID represents a unique molecule.

Relationships to Other Record Types

For each het group that appears in the entry, the corresponding HET, HETNAM, HETSYN, FORMUL, HETATM, and CONECT records must appear, if applicable. LINK records may also appear.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
HET    TRS    975       8
HET    STA  I   4      25     PART_OF: HIV INHIBITOR;
HET    FUC  Y   1      10     PART_OF: NONOATE COMPLEX; L-FUCOSE       
HET    GAL  Y   2      11     PART_OF: NONOATE COMPLEX                 
HET    NAG  Y   3      15     PART_OF: NONOATE COMPLEX                 
HET    FUC  Y   4      10     PART_OF: NONOATE COMPLEX                 
HET    NON  Y   5      12     PART_OF: NONOATE COMPLEX
HET    UNX  A 161       1     PSEUDO CARBON ATOM OF UNKNOWN LIGAND
HET    UNX  A 162       1     PSEUDO CARBON ATOM OF UNKNOWN LIGAND
HET    UNX  A 163       1     PSEUDO CARBON ATOM OF UNKNOWN LIGAND

Known Problems

Even though groups may be chemically bound to others with loss of atoms (e.g., H, O), the PDB has only one representation for the complete molecule. However, a few small groups are represented separately as ions, groups, and molecules.

PDB does not include CAS registry and Cambridge Structural Database (CSD) accession numbers.

Large het groups are broken into recognizable sub-groups to obviate difficulties associated with the limitations of the atom naming conventions used by the PDB. The description of how to reassemble the full molecule is addressed in a REMARK. The token PART_OF and use of segment identifiers may help to describe the larger entity.


HETNAM

Overview

This record gives the chemical name of the compound with the given hetID.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                 
-------------------------------------------------------------------------
 1 -  6        Record name     "HETNAM"                                  
 9 - 10        Continuation    continuation   Allows concatenation of    
                                              multiple records.          
12 - 14        LString(3)      hetID          Het identifier,            
                                              right-justified.           
16 - 70        String          text           Chemical name.             

Details

* Each hetID is assigned a unique chemical name for the HETNAM record.

* Other names for the group are given on HETSYN records.

* PDB follows IUPAC/IUB naming conventions to describe groups systematically.

* Continuation of chemical names onto subsequent records is allowed.

* Only one HETNAM record is included for a given hetID, even if the same hetID appears on more than one HET record.

Verification/Validation/Value Authority Control

For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM and CONECT records must appear. The HETNAM record is generated automatically by PDB using the het group dictionary and information from HETATM records.

Relationships to Other Record Types

For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear. HETSYN and LINK records may also appear.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
HETNAM     GLC GLUCOSE
HETNAM     SAD BETA-METHYLENE SELENAZOLE-4-CARBOXAMIDE ADENINE
HETNAM  2  SAD DINUCLEOTIDE
HETNAM     UNX UNKNOWN ATOM OR ION


HETSYN

Overview

This record provides synonyms, if any, for the compound in the corresponding (i.e., same hetID) HETNAM record. This is to allow greater flexibility in searching for HET groups.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                 
----------------------------------------------------------------------
 1 -  6        Record name     "HETSYN"                                  
 9 - 10        Continuation    continuation   Allows concatenation of    
                                              multiple records.          
12 - 14        LString(3)      hetID          Het identifier,            
                                              right-justified.           
16 - 70        SList           hetSynonyms    List of synonyms.          

Details

* This is not guaranteed to be a complete list of possible synonyms, but is uniform across the PDB. New synonyms may be added. The list can be continued onto additional HETSYN records. Even if the same hetID appears on more than one HET record, only one set of HETSYN records is included for the hetID.

Verification/Validation/Value Authority Control

For each HETSYN record in the entry, the corresponding HET, HETNAM, FORMUL, HETATM and CONECT records must appear.

Relationships to Other Record Types

If there is a HETSYN record there must be corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records. LINK records may also appear.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
HETSYN     NAD NICOTINAMIDE ADENINE DINUCLEOTIDE
HETSYN     COA COA
HETSYN     CMP CYCLIC AMP; CYCLIC ADENOSINE MONOPHOSPHATE
HETSYN     TRS TRIS BUFFER; TRISAMINE; 
HETSYN   2 TRS TRIS(HYDROXYMETHYL)AMINOMETHANE; TRIMETHYLOL
HETSYN   3 TRS AMINOMETHANE


FORMUL

Overview

The FORMUL record presents the chemical formula and charge of a non-standard group. (The formulas for the standard residues are given in Appendix 5.)

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                        
---------------------------------------------------------------------------
 1 -  6        Record name     "FORMUL"                                         
 9 - 10        Integer         compNum        Component number.                 
13 - 15        LString(3)      hetID          Het identifier.                   
17 - 18        Integer         continuation   Continuation number.              
19             Character       asterisk       "*" for water.                    
20 - 70        String          text           Chemical formula.                 

Details

* The elements of the chemical formula are given in the order C, H, N, and O, with other elements following in alphabetical order, each separated by a single blank.

* The number of each atom type present immediately follows its chemical symbol with no intervening blank.

* Each set of SEQRES records and each HET group is assigned a component number in an entry. These numbers are assigned serially, beginning with 1 for the first set of SEQRES records. In addition:

- If a HET group is presented on a SEQRES record its FORMUL is assigned the component number of the chain in which it appears.
- If the HET group occurs more than once and is not presented on SEQRES records, the component number of its first occurrence is used.

* All occurrences of the HET group within a chain are grouped together with a multiplier. The remaining occurrences are also grouped with a multiplier. The sum of the multipliers is the number equaling the number of times that that HET group appears in the entry.

* The "*" in column 19 is used if the HET group is water or UNX, indicating that it should be excluded from the molecular weight calculation.

* A continuation field is provided in the event that more space is needed for the formula. Columns 17 - 18 are used in order to maintain continuity with the existing format.

Verification/Validation/Value Authority Control

For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear. The FORMUL record is generated automatically by PDB processing programs using the het group template file and information from HETATM records.

Relationships to Other Record Types

For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
FORMUL   2  SO4    2(O4 S1 2-)
FORMUL   3  GLC    C6 H12 O6
FORMUL   3  FOL    2(C19 H17 N7 O6 2-)
FORMUL   4   CL    2(CL1 1-) 
FORMUL   5   CA    CA1 2+ 
FORMUL   6  HOH   *429(H2 O1)
FORMUL   3  UNX   *3(X1) 
FORMUL   4  HOH   *256(H2 O1) 
FORMUL   1  ACE    C2 H3 O1 
FORMUL   2  ACE    C2 H3 O1

Known Problems

Partially deuterated centers are not well represented in this record.


5. Secondary Structure Section

The secondary structure section of a PDB file describes helices, sheets, and turns found in protein and polypeptide structures.


HELIX

Overview

HELIX records are used to identify the position of helices in the molecule. Helices are both named and numbered. The residues where the helix begins and ends are noted, as well as the total length.

Record Format

COLUMNS        DATA TYPE       FIELD           DEFINITION                           
---------------------------------------------------------------------------------
 1 -  6        Record name     "HELIX "                                             
 8 - 10        Integer         serNum          Serial number of the helix.          
                                               This starts at 1 and increases       
                                               incrementally.                       
12 - 14        LString(3)      helixID         Helix identifier.  In addition       
                                               to a serial number, each helix is    
                                               given an alphanumeric character 
                                               helix identifier.  
16 - 18        Residue name    initResName     Name of the initial residue.         
20             Character       initChainID     Chain identifier for the chain       
                                               containing this helix.               
22 - 25        Integer         initSeqNum      Sequence number of the initial       
                                               residue.                             
26             AChar           initICode       Insertion code of the initial        
                                               residue.                             
28 - 30        Residue name    endResName      Name of the terminal residue of      
                                               the helix.                           
32             Character       endChainID      Chain identifier for the chain       
                                               containing this helix.               
34 - 37        Integer         endSeqNum       Sequence number of the terminal      
                                               residue.                             
38             AChar           endICode        Insertion code of the terminal       
                                               residue.                             
39 - 40        Integer         helixClass           Helix class (see below).             
41 - 70        String          comment         Comment about this helix.            
72 - 76        Integer         length          Length of this helix.                

Details

* Additional HELIX records with different serial numbers and identifiers occur if more than one helix is present.

* The initial residue is the N-terminal residue of the helix.

* Helices are classified as follows:

           TYPE OF HELIX             CLASS NUMBER (COLUMNS 39 - 40)
     --------------------------------------------------------------
     Right-handed alpha (default)                1
     Right-handed omega                          2
     Right-handed pi                             3
     Right-handed gamma                          4
     Right-handed 310                            5
     Left-handed alpha                           6
     Left-handed omega                           7
     Left-handed gamma                           8
     27 ribbon/helix                             9
     Polyproline                                10

Verification/Validation/Value Authority Control

HELIX records are now being generated automatically by PDB using the Kabsch and Sander algorithm [Kabsch and Sander, Biopolymers 22: 2577-2637 (1983)], although they may be provided by the depositor instead. PDB verifies that named residues exist in the ATOM records.

Relationships to Other Record Types

There may be related information in the REMARKs.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890123456
HELIX    1  HA GLY A   86  GLY A   94  1                                   9
HELIX    2  HB GLY B   86  GLY B   94  1                                   9

Known Problems

PDB is considering addition of some new information related to HELIX, in order to present more complete structural information. Please comment on the suggestion of adding a new record which would present the various domain types found in the molecule, e.g., Residues 12 --> 120: alpha/beta.


SHEET

Overview

SHEET records are used to identify the position of sheets in the molecule. Sheets are both named and numbered. The residues where the sheet begins and ends are noted.

Record Format

COLUMNS        DATA TYPE       FIELD           DEFINITION                          
----------------------------------------------------------------------------------
 1 -  6        Record name     "SHEET "                                            
 8 - 10        Integer         strand          Strand number which starts at 1 for 
                                               each strand within a sheet and      
                                               increases by one.                   
12 - 14        LString(3)      sheetID         Sheet identifier.                   
15 - 16        Integer         numStrands      Number of strands in sheet.         
18 - 20        Residue name    initResName     Residue name of initial residue.    
22             Character       initChainID     Chain identifier of initial residue 
                                               in strand.                          
23 - 26        Integer         initSeqNum      Sequence number of initial residue  
                                               in strand.                          
27             AChar           initICode       Insertion code of initial residue   
                                               in strand.                          
29 - 31        Residue name    endResName      Residue name of terminal residue.   
33             Character       endChainID      Chain identifier of terminal        
                                               residue.                            
34 - 37        Integer         endSeqNum       Sequence number of terminal residue.
38             AChar           endICode        Insertion code of terminal residue. 
39 - 40        Integer         sense           Sense of strand with respect to     
                                               previous strand in the sheet. 0     
                                               if first strand, 1 if parallel,     
                                               -1 if anti-parallel.               
42 - 45        Atom            curAtom         Registration. Atom name in current 
                                               strand.         
46 - 48        Residue name    curResName      Registration. Residue name in 
                                               current strand.      
50             Character       curChainId      Registration. Chain identifier in 
                                               current strand.  
51 - 54        Integer         curResSeq       Registration. Residue sequence 
                                               number in current strand.          
55             AChar           curICode        Registration. Insertion code in 
                                               current strand.    
57 - 60        Atom            prevAtom        Registration. Atom name in 
                                               previous strand.        
61 - 63        Residue name    prevResName     Registration. Residue name in 
                                               previous strand.     
65             Character       prevChainId     Registration. Chain identifier in 
                                               previous strand.                   
66 - 69        Integer         prevResSeq      Registration. Residue sequence
                                               number in previous strand.         
70             AChar           prevICode       Registration. Insertion code in 
                                               previous strand.   

Details

* The initial residue for a strand is its N-terminus. Strand registration information is provided in columns 39 - 70. Strands are listed starting with one edge of the sheet and continuing to the spatially adjacent strand.

* The sense in columns 39 - 40 indicates whether strand n is parallel (sense = 1) or anti-parallel (sense = -1) to strand n-1. Sense is equal to zero (0) for the first strand of a sheet.

* The registration (columns 42 - 70) of strand n to strand n-1 may be specified by one hydrogen bond between each such pair of strands. This is done by providing the hydrogen bonding between the current and previous strands. No registration information should be provided for the first strand.

* For structures which form a closed sheet (beta-barrel), the first strand is repeated as the last strand. An explanatory remark is included in the REMARK section.

* Split strands, or strands with two or more runs of residues from discontinuous parts of the amino acid sequence, are explicitly listed. Provide a description to be included in the REMARK section.

Verification/Validation/Value Authority Control

SHEET records are now being generated automatically by PDB using the Kabsch and Sander algorithm [Kabsch and Sander, Biopolymers 22: 2577-2637 (1983)], although they may be provided by the depositor instead. PDB verifies that named residues exist in the ATOM records.

Relationships to Other Record Types

If the entry contains bifurcated sheets or beta-barrels, the relevant REMARK records must be provided. See the REMARK section for details.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SHEET    1   A 5 THR A 107  ARG A 110  0
SHEET    2   A 5 ILE A  96  THR A  99 -1  N  LYS A  98   O  THR A 107
SHEET    3   A 5 ARG A  87  SER A  91 -1  N  LEU A  89   O  TYR A  97
SHEET    4   A 5 TRP A  71  ASP A  75 -1  N  ALA A  74   O  ILE A  88
SHEET    5   A 5 GLY A  52  PHE A  56 -1  N  PHE A  56   O  TRP A  71
SHEET    1   B 5 THR B 107  ARG B 110  0
SHEET    2   B 5 ILE B  96  THR B  99 -1  N  LYS B  98   O  THR B 107
SHEET    3   B 5 ARG B  87  SER B  91 -1  N  LEU B  89   O  TYR B  97
SHEET    4   B 5 TRP B  71  ASP B  75 -1  N  ALA B  74   O  ILE B  88
SHEET    5   B 5 GLY B  52  ILE B  55 -1  N  ASP B  54   O  GLU B  73

The sheet presented as BS1 below is an eight-stranded beta-barrel. This is represented by a nine-stranded sheet in which the first and last strands are identical.

SHEET    1 BS1 9 VAL    13  ILE    17  0                               
SHEET    2 BS1 9 ALA    70  ILE    73  1  O  TRP    72   N  ILE    17  
SHEET    3 BS1 9 LYS   127  PHE   132  1  O  ILE   129   N  ILE    73  
SHEET    4 BS1 9 GLY   221  ASP   225  1  O  GLY   221   N  ILE   130  
SHEET    5 BS1 9 VAL   248  GLU   253  1  O  PHE   249   N  ILE   222  
SHEET    6 BS1 9 LEU   276  ASP   278  1  N  LEU   277   O  GLY   252  
SHEET    7 BS1 9 TYR   310  THR   318  1  O  VAL   317   N  ASP   278  
SHEET    8 BS1 9 VAL   351  TYR   356  1  O  VAL   351   N  THR   318  
SHEET    9 BS1 9 VAL    13  ILE    17  1  N  VAL    14   O  PRO   352  

The sheet structure of this example is bifurcated. In order to represent this feature, two sheets are defined. Strands 2 and 3 of BS7 and BS8 are identical.

SHEET    1 BS7 3 HIS   662  THR   665  0                               
SHEET    2 BS7 3 LYS   639  LYS   648 -1  N  PHE   643   O  HIS   662  
SHEET    3 BS7 3 ASN   596  VAL   600 -1  N  TYR   598   O  ILE   646  
SHEET    1 BS8 3 ASN   653  TRP   656  0                               
SHEET    2 BS8 3 LYS   639  LYS   648 -1  N  LYS   647   O  THR   655  
SHEET    3 BS8 3 ASN   596  VAL   600 -1  N  TYR   598   O  ILE   646  


TURN

Overview

The TURN records identify turns and other short loop turns which normally connect other secondary structure segments.

Record Format

COLUMNS        DATA TYPE      FIELD          DEFINITION                             
----------------------------------------------------------------------------------
 1 -  6        Record name    "TURN  "                                              
 8 - 10        Integer        seq            Turn number; starts with 1 and         
                                             increments by one.                     
12 - 14        LString(3)     turnId         Turn identifier                        
16 - 18        Residue name   initResName    Residue name of initial residue in     
                                             turn.                                  
20             Character      initChainId    Chain identifier for the chain         
                                             containing this turn.                  
21 - 24        Integer        initSeqNum     Sequence number of initial residue     
                                             in turn.                               
25             AChar          initICode      Insertion code of initial residue in   
                                             turn.                                  
27 - 29        Residue name   endResName     Residue name of terminal residue of    
                                             turn.                                  
31             Character      endChainId     Chain identifier for the chain         
                                             containing this turn.                  
32 - 35        Integer        endSeqNum      Sequence number of terminal residue    
                                             of turn.                               
36             AChar          endICode       Insertion code of terminal residue     
                                             of turn.                               
41 - 70        String         comment        Associated comment.                    

Details

* Turns include those sets of residues which form beta turns, i.e., have a hydrogen bond linking (C-O)i to (N-H)i+3. Turns which link residue i to i+2 (gamma-bends) may also be included. Others may be also be classified as turns.

* The initial residue is the N-terminus.

Verification/Validation/Value Authority Control

The validation program checks the number of residues in the given turn. PDB verifies that named residues exist in the ATOM records.

Relationships to Other Record Types

There may be related information in the REMARKs.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
TURN     1 S1A GLY A  16  GLN A  18     SURFACE                       
TURN     2 FLA ILE A  50  GLY A  52     FLAP                          
TURN     3 S2A ILE A  66  HIS A  69     SURFACE                       
TURN     4 S1B GLY B  16  GLN B  18     SURFACE                       
TURN     5 FLB ILE B  50  GLY B  52     FLAP                          
TURN     6 S2B ILE B  66  HIS B  69     SURFACE                       


6. Connectivity Annotation Section

The connectivity annotation section allows the depositors to specify the existence and location of disulfide bonds and other linkages.


SSBOND

Overview

The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.

Record Format

COLUMNS       DATA TYPE       FIELD          DEFINITION                           
----------------------------------------------------------------------------
 1 -  6       Record name     "SSBOND"                                            
 8 - 10       Integer         serNum         Serial number.                      
12 - 14       LString(3)      "CYS"          Residue name.                        
16            Character       chainID1       Chain identifier.                    
18 - 21       Integer         seqNum1        Residue sequence number.             
22            AChar           icode1         Insertion code.                      
26 - 28       LString(3)      "CYS"          Residue name.                        
30            Character       chainID2       Chain identifier.                    
32 - 35       Integer         seqNum2        Residue sequence number.             
36            AChar           icode2         Insertion code.                      
60 - 65       SymOP           sym1           Symmetry operator for 1st residue.   
67 - 72       SymOP           sym2           Symmetry operator for 2nd residue.   

Details

* Bond distances between the sulfur atoms must be close to expected values.

* The cysteine closer to the N-terminal is listed first in each intra-chain pair. The cysteine which occurs first in the coordinate entry is listed first for inter-chain pairs.

* sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the residue.

Verification/Validation/Value Authority Control

PDB processing programs generate these records automatically. If the depositor supplies these records, they are compared to those generated and the depositor is notified of any differences.

Relationships to Other Record Types

CONECT records are generated for the disulfide bonds when SG atoms of both cysteines are present in the coordinate records. If symmetry operators are given to generate one of the residues involved in the disulfide bond, REMARK290 defines the symmetry transformation.

Example

         1         2         3         4         5         6         7            
123456789012345678901234567890123456789012345678901234567890123456789012          
SSBOND   1 CYS E   48    CYS E   51                          2555  
SSBOND   2 CYS E  252    CYS E  285                                               

Known Problems

If SG of cysteine is disordered then there are possible alternate linkages. PDB's practice is to put together all possible SSBOND records. This is problematic because the alternate location identifier is not specified in the SSBOND record.


LINK

Overview

The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. This record supplements information given in CONECT records and is provided here for convenience in searching.

Record Format

COLUMNS        DATA TYPE       FIELD       DEFINITION                              
--------------------------------------------------------------------------------
 1 -  6        Record name     "LINK  "                                            
13 - 16        Atom            name1       Atom name.                              
17             Character       altLoc1     Alternate location indicator.           
18 - 20        Residue name    resName1    Residue name.                           
22             Character       chainID1    Chain identifier.                       
23 - 26        Integer         resSeq1     Residue sequence number.                
27             AChar           iCode1      Insertion code.                         
43 - 46        Atom            name2       Atom name.                              
47             Character       altLoc2     Alternate location indicator.           
48 - 50        Residue name    resName2    Residue name.                           
52             Character       chainID2    Chain identifier.                       
53 - 56        Integer         resSeq2     Residue sequence number.                
57             AChar           iCode2      Insertion code.                         
60 - 65        SymOP           sym1        Symmetry operator for 1st atom.         
67 - 72        SymOP           sym2        Symmetry operator for 2nd atom.         

Details

* The atoms involved in bonds between HET groups or between a HET group and standard residue are listed.

* Interresidue linkages not implied by the primary structure are listed (e.g., reduced peptide bond).

* Non-standard linkages between residues, e.g., side-chain to side-chain, are listed.

* Each LINK record specifies one linkage.

* These records do not specify connectivity within a HET group (see CONECT), hydrogen bonds (see HYDBND), or disulfide bridges (see SSBOND).

* Hydrogen bonds and salt bridges are described on HYDBND and SLTBRG records, respectively.

* sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the atom.

* For NMR entries only one set (or model) of LINK records will be supplied.

Verification/Validation/Value Authority Control

The distance between the pair of atoms listed must be consistent with the bonding.

Relationships to Other Record Types

CONECT records are generated from LINKs when both atoms are present in the entry. If symmetry operators are given to generate one of the residues involved in the bond, REMARK 290 defines the symmetry transformation.

Example

         1         2         3         4         5         6         7
123456789012345678901234567890123456789012345678901234567890123456789012
LINK         O1  DDA     1                 C3  DDL     2      
LINK        MN    MN   391                 OE2 GLU   217            2565


HYDBND

Overview

The HYDBND records specify hydrogen bonds in the entry.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
---------------------------------------------------------------------------------
 1 -  6        Record name     "HYDBND"                                          
13 - 16        Atom            name1          Atom name.                         
17             Character       altLoc1        Alternate location indicator.      
18 - 20        Residue name    resName1       Residue name.                      
22             Character       Chain1         Chain identifier.                  
23 - 27        Integer         resSeq1        Residue sequence number.           
28             AChar           ICode1         Insertion code.                    
30 - 33        Atom            nameH          Hydrogen atom name.                
34             Character       altLocH        Alternate location indicator.      
36             Character       ChainH         Chain identifier.                  
37 - 41        Integer         resSeqH        Residue sequence number.           
42             AChar           iCodeH         Insertion code.                    
44 - 47        Atom            name2          Atom name.                         
48             Character       altLoc2        Alternate location indicator.      
49 - 51        Residue name    resName2       Residue name.                      
53             Character       chainID2       Chain identifier.                  
54 - 58        Integer         resSeq2        Residue sequence number.           
59             AChar           iCode2         Insertion code.                    
60 - 65        SymOP           sym1           Symmetry operator for 1st          
                                              non-hydrogen atom.         
67 - 72        SymOP           sym2           Symmetry operator for 2nd 
                                              non-hydrogen atom.     

Details

* The hydrogen bonds listed normally are those supplied by the depositor.

* The atoms forming the hydrogen bond are listed on the HYDBND record.

* Each record has place for three atom specifications.

* Columns 13 - 28 and 44 - 59 are for the atoms associated with the hydrogen atom of the hydrogen bond.

* If the coordinates of the hydrogen atom itself are presented in the entry, that atom is specified in columns 30 - 42.

* For nucleic acids, Watson-Crick hydrogen bonds between bases may be listed, but this is optional.

* sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the atom. For hydrogen atoms use the symmetry operator of the heavy atom to which it is bonded.

Verification/Validation/Value Authority Control

The distance between the atoms listed must be consistent with the bonding.

Relationships to Other Record Types

CONECT records are generated consistent with the bond type. If symmetry operators are given to generate one of the residues involved in the hydrogen bond, REMARK200 defines the symmetry transformation.

Example

         1         2         3         4         5         6         7
123456789012345678901234567890123456789012345678901234567890123456789012
HYDBND       N   LEU     10                AO3* NDP    501
HYDBND       NH2 ARG    111                 OD1 ASP    149   1555


SLTBRG

Overview

The SLTBRG records specify salt bridges in the entry.

Record Format

COLUMNS       DATA TYPE       FIELD         DEFINITION                               
---------------------------------------------------------------------------------
 1 -  6       Record name     "SLTBRG"                                               
13 - 16       Atom            atom1         First atom name.                         
17            Character       altLoc1       Alternate location indicator.            
18 - 20       Residue name    resName1      Residue name.                            
22            Character       chainID1      Chain identifier.                        
23 - 26       Integer         resSeq1       Residue sequence number.                 
27            AChar           iCode1        Insertion code.                          
43 - 46       Atom            atom2         Second atom name.                        
47            Character       altLoc2       Alternate location indicator.            
48 - 50       Residue name    resName2      Residue name.                            
52            Character       chainID2      Chain identifier.                        
53 - 56       Integer         resSeq2       Residue sequence number.                 
57            AChar           iCode2        Insertion code.                          
60 - 65       SymOP           sym1          Symmetry operator for 1st atom.          
67 - 72       SymOP           sym2          Symmetry operator for 2nd atom.          

Details

* Salt bridges listed normally are those provided by the depositor.

* The two atoms forming the salt bridge through their electrostatic interactions are specified.

* No distinction is made as to which atom has excess positive or negative charge.

* sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the atom.

Verification/Validation/Value Authority Control

The distance between the pair of atoms listed must be consistent with the bonding.

Relationships to Other Record Types

CONECT records are generated consistent with the bond type. If symmetry operators are given to generate one of the residues involved in the salt bridge, REMARK 290 defines the symmetry transformation.

Example

         1         2         3         4         5         6         7
123456789012345678901234567890123456789012345678901234567890123456789012
SLTBRG       O   GLU    10                 NZ  LYS  115
SLTBRG       O   GLU    10                 NZ  LYS  115             3654


CISPEP

Overview

CISPEP records specify the prolines and other peptides found to be in the cis conformation. This record replaces the use of footnote records to list cis peptides.

Record Format

COLUMNS       DATA TYPE       FIELD        DEFINITION                
-------------------------------------------------------------------------
 1 -  6       Record name     "CISPEP"                               
 8 - 10       Integer         serNum       Record serial number.   
12 - 14       LString(3)      pep1         Residue name.             
16            Character       chainID1     Chain identifier.         
18 - 21       Integer         seqNum1      Residue sequence number.  
22            AChar           icode1       Insertion code.           
26 - 28       LString(3)      pep2         Residue name.  
30            Character       chainID2     Chain identifier.         
32 - 35       Integer         seqNum2      Residue sequence number.  
36            AChar           icode2       Insertion code.           
44 - 46       Integer         modNum       Identifies the specific model.
54 - 59       Real(6.2)       measure      Measure of the angle in   
                                           degrees.

Details

* Cis peptides are those with omega angles of 0°±30°. Deviations larger than 30° are listed in REMARK 500.

* Each cis peptide is listed on a separate line, with an incrementally ascending sequence number.

Verification/Validation/Value Authority Control

PDB generates these records automatically, however, the depositor may wish to list cis peptides at the time of submission.

Relationships to Other Record Types

CISPEP is replacing the footnote which previously contained this information.

Peptide bonds which deviate significantly from either cis or trans conformation are annotated in REMARK 500.

Example

         1         2         3         4         5         6         7            
1234567890123456789012345678901234567890123456789012345678901234567890            
CISPEP   1 GLY A  116    GLY A  117          0        18.50                 
CISPEP   2 THR D   92    PRO D   93          0       359.80


7. Miscellaneous Features Section

The miscellaneous features section describes features in the molecule such as the active site. Other features may be described in the remarks section but are not given a specific record type so far.


SITE

Overview

The SITE records supply the identification of groups comprising important sites in the macromolecule.

Record Format

COLUMNS       DATA TYPE       FIELD       DEFINITION                              
---------------------------------------------------------------------------------
 1 -  6       Record name     "SITE  "                                            
 8 - 10       Integer         seqNum      Sequence number.                        
12 - 14       LString(3)      siteID      Site name.                              
16 - 17       Integer         numRes      Number of residues comprising site.     
19 - 21       Residue name    resName1    Residue name for first residue          
                                          comprising site.                        
23            Character       chainID1    Chain identifier for first residue      
                                          comprising site.                        
24 - 27       Integer         seq1        Residue sequence number for first       
                                          residue comprising site.                
28            AChar           iCode1      Insertion code for first residue        
                                          comprising site.                        
30 - 32       Residue name    resName2    Residue name for second residue         
                                          comprising site.                        
34            Character       chainID2    Chain identifier for second residue     
                                          comprising site.                        
35 - 38       Integer         seq2        Residue sequence number for second      
                                          residue comprising site.                
39            AChar           iCode2      Insertion code for second residue       
                                          comprising site.                        
41 - 43       Residue name    resName3    Residue name for third residue          
                                          comprising site.                        
45            Character       chainID3    Chain identifier for third residue      
                                          comprising site.                        
46 - 49       Integer         seq3        Residue sequence number for third       
                                          residue comprising site.                
50            AChar           iCode3      Insertion code for third residue        
                                          comprising site.                        
52 - 54       Residue name    resName4    Residue name for fourth residue         
                                          comprising site.                        
56            Character       chainID4    Chain identifier for fourth residue     
                                          comprising site.                        
57 - 60       Integer         seq4        Residue sequence number for fourth      
                                          residue comprising site.                
61            AChar           iCode4      Insertion code for fourth residue       
                                          comprising site.                        

Details

* Site records specify residues comprising catalytic, cofactor, anticodon, regulatory or other important sites.

* The sequence number (columns 8 - 10) is reset to 1 for each new site.

* SITE identifiers (columns 12 - 14) should be fully explained in a remark.

* If a site is comprised of more than four residues, these may be specified on additional records bearing the same site identifier.

* SITE records can include HET groups.

Verification/Validation/Value Authority Control

Every SITE must have a corresponding remark that describes it. The numbering of sequential SITE records and format of each one is verified, as well as the existence of each residue in the ATOM records.

Relationships to Other Record Types

Each listed SITE needs a corresponding REMARK 800 that details its significance.

Example

         1         2         3         4         5         6         7            
1234567890123456789012345678901234567890123456789012345678901234567890            
SITE     1 DTA  3 ASP A  25  THR A  26  GLY A  27         
SITE     1 DTB  3 ASP B  25  THR B  26  GLY B  27         
SITE     1   A  4   U A  44    C A  46    G A  61    U A 118
SITE     1 ZN1  5 CYS A  97  CYS A 100  CYS A 103  CYS 1 111 
SITE     2 ZN1  5  ZN A 375


8. Crystallographic and Coordinate Transformation Section

The Crystallographic Section describes the geometry of the crystallographic experiment and the coordinate system transformations.


CRYST1

Overview

The CRYST1 record presents the unit cell parameters, space group, and Z value. If the structure was not determined by crystallographic means, CRYST1 simply defines a unit cube.

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION        
-------------------------------------------------------------
 1 -  6       Record name    "CRYST1"                        
 7 - 15       Real(9.3)      a             a (Angstroms).     
16 - 24       Real(9.3)      b             b (Angstroms).     
25 - 33       Real(9.3)      c             c (Angstroms).     
34 - 40       Real(7.2)      alpha         alpha (degrees).   
41 - 47       Real(7.2)      beta          beta (degrees).    
48 - 54       Real(7.2)      gamma         gamma (degrees).   
56 - 66       LString        sGroup        Space group.       
67 - 70       Integer        z             Z value.           

Details

* If the coordinate entry describes a structure determined by a technique other than crystallography, CRYST1 contains a = b = c = 1.0, alpha = beta = gamma = 90 degrees, space group = P 1, and Z = 1.

* The Hermann-Mauguin space group symbol is given without parenthesis, e.g., P 43 21 2. Please note that the screw axis is described as a two digit number.

* The full international Hermann-Mauguin symbol is used, e.g., P 1 21 1 instead of P 21.

* For a rhombohedral space group in the hexagonal setting, the lattice type symbol used is H.

* The Z value is the number of polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain.

As an example, given two chains A and B, each with a different sequence, and the space group P 2 that has two equipoints in the standard unit cell, the following table gives the correct Z value.
       Asymmetric Unit Content     Z value   
       -----------------------------------
                 A                    2         
                 AA                   4         
                 AB                   2         
                 AAB                  4         
                 AABB                 4         

* In the case of a polycrystalline fiber diffraction study, CRYST1 and SCALE contain the normal unit cell data.

Verification/Validation/Value Authority Control

The given space group and Z values are checked during processing for correctness and internal consistency. The calculated SCALE is compared to that supplied by the depositor. Packing is also computed, and close contacts of symmetry-related molecules are diagnosed.

Relationships to Other Record Types

The unit cell parameters are used to calculate SCALE. If the EXPDTA record is NMR, THEORETICAL MODEL, or FIBER DIFFRACTION, FIBER, the CRYST1 record is predefined as a = b = c = 1.0, alpha = beta = gamma = 90 degrees, space group = P 1 and Z = 1. In these cases, an explanatory REMARK must also appear in the entry. Some fiber diffraction structures will be done this way, while others will have a CRYST1 record containing measured values.

Example

         1         2         3         4         5         6         7 
1234567890123456789012345678901234567890123456789012345678901234567890 
CRYST1   52.000   58.600   61.900  90.00  90.00  90.00 P 21 21 21    8 
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1 
CRYST1   42.544   69.085   50.950  90.00  95.55  90.00 P 1 21 1      2

Known Problems

No standard deviations are given.


ORIGXn

Overview

The ORIGXn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.

Record Format

COLUMNS       DATA TYPE       FIELD          DEFINITION                           
-------------------------------------------------------------
 1 -  6       Record name     "ORIGXn"       n=1, 2, or 3                         
11 - 20       Real(10.6)      o[n][1]        On1                                  
21 - 30       Real(10.6)      o[n][2]        On2                                  
31 - 40       Real(10.6)      o[n][3]        On3                                  
46 - 55       Real(10.5)      t[n]           Tn                                   

Details

* The PDB supplies this information even if the transformation is an identity transformation (unit matrix, null vector). See the SCALE section of this document for a definition of the default orthogonal Angstroms system.

* If the original submitted coordinates are Xsub, Ysub, Zsub and the orthogonal Angstroms coordinates contained in the data entry are X, Y, Z, then:

Xsub = O11X + O12Y + O13Z + T1
Ysub = O21X + O22Y + O23Z + T2
Zsub = O31X + O32Y + O33Z + T3

* Appendix 2 details the derivation of the ORIGX coordinate transformation.

Verification/Validation/Value Authority Control

If the coordinates are submitted in the same orthogonal Angstrom coordinate frame as they appear in the entry (the usual case), then ORIGX is an identity matrix with a null translation vector. If the transformation is not an identity matrix with a null translation vector, then applying this transformation to the coordinates in the entry yields the coordinates in the original deposited file.

Relationships to Other Record Types

ORIGX relates the coordinates in the ATOM and HETATM records to the coordinates in the submitted file.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
ORIGX1      0.963457  0.136613  0.230424       16.61000               
ORIGX2     -0.158977  0.983924  0.081383       13.72000               
ORIGX3     -0.215598 -0.115048  0.969683       37.65000               


SCALEn

Overview

The SCALEn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates as contained in the entry to fractional crystallographic coordinates. Non-standard coordinate systems should be explained in the remarks.

Record Format

COLUMNS       DATA TYPE      FIELD          DEFINITION                  
----------------------------------------------------------------
 1 -  6       Record name    "SCALEn"       n=1, 2, or 3                
11 - 20       Real(10.6)     s[n][1]        Sn1                         
21 - 30       Real(10.6)     s[n][2]        Sn2                         
31 - 40       Real(10.6)     s[n][3]        Sn3                         
46 - 55       Real(10.5)     u[n]           Un                          

Details

* The standard orthogonal Angstroms coordinate system used by the PDB is related to the axial system of the unit cell supplied (CRYST1 record) by the following definition:

* If vector a, vector b, vector c describe the crystallographic cell edges, and vector A, vector B, vector C are unit cell vectors in the default orthogonal Angstroms system, then vector A, vector B, vector C and vector a, vector b, vector c have the same origin; vector A is parallel to vector a, vector B is parallel to vector C times vector A, and vector C is parallel to vector a times vector b (i.e., vector c*).

* If the orthogonal Angstroms coordinates are X, Y, Z, and the fractional cell coordinates are xfrac, yfrac, zfrac, then:

xfrac = S11X + S12Y + S13Z + U1
yfrac = S21X + S22Y + S23Z + U2
zfrac = S31X + S32Y + S33Z + U3

* For NMR, fiber diffraction - fiber sample, and theoretical model entries, SCALE is given as an identity matrix with no translation.

* Appendix 2 details the derivation of the SCALE coordinate transformation.

Verification/Validation/Value Authority Control

The inverse of the determinant of the SCALE matrix equals the volume of the cell. This volume is calculated and compared to the SCALE matrix supplied by the depositor.

Relationships to Other Record Types

The SCALE transformation is related to the CRYST1 record, as the inverse of the determinant of the SCALE matrix equals the cell volume.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SCALE1      0.019231  0.000000  0.000000        0.00000               
SCALE2      0.000000  0.017065  0.000000        0.00000               
SCALE3      0.000000  0.000000  0.016155        0.00000               


MTRIXn

Overview

The MTRIXn (n = 1, 2, or 3) records present transformations expressing non-crystallographic symmetry.

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                          
-------------------------------------------------------------------------------
 1 -  6       Record name    "MTRIXn"      n=1, 2, or 3                        
 8 - 10       Integer        serial        Serial number.                      
11 - 20       Real(10.6)     m[n][1]       Mn1                                 
21 - 30       Real(10.6)     m[n][2]       Mn2                                 
31 - 40       Real(10.6)     m[n][3]       Mn3                                 
46 - 55       Real(10.5)     v[n]          Vn                                  
60            Integer        iGiven        1 if coordinates for the            
                                           representations which are           
                                           approximately related by the        
                                           transformations of the molecule are 
                                           contained in the entry.  Otherwise, 
                                           blank.                              

Details

* The MTRIX transformations operate on the coordinates in the entry to yield equivalent representations of the molecule in the same coordinate frame. One trio of MTRIX records with a constant serial number is given for each non-crystallographic symmetry operation defined. If coordinates for the representations which are approximately related by the given transformation are contained in the file, the iGiven field is set to 1. Otherwise, this field is blank.

* A corresponding REMARK must appear which describes the transformation.

Verification/Validation/Value Authority Control

The PDB verifies all MTRIX records by applying the given transformation and determining the RMSD between the calculated and supplied coordinates if iGiven is equal to 1. If iGiven is blank, PDB verifies MTRIX by checking the packing of the generated molecules.

Relationships to Other Record Types

A corresponding REMARK must appear which describes the transformation.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
MTRIX1   1 -1.000000  0.000000 -0.000000        0.00001    1          
MTRIX2   1 -0.000000  1.000000  0.000000        0.00002    1          
MTRIX3   1  0.000000 -0.000000 -1.000000        0.00002    1          


TVECT

Overview

The TVECT records present the translation vector for infinite covalently connected structures.

Record Format

COLUMNS       DATA TYPE      FIELD       DEFINITION                      
-------------------------------------------------------------------------
 1 -  6       Record name    "TVECT "                                    
 8 - 10       Integer        serial      Serial number.                  
11 - 20       Real(10.5)     t[1]        Components of translation       
                                         vector.                         
21 - 30       Real(10.5)     t[2]        Components of translation       
                                         vector.                         
31 - 40       Real(10.5)     t[3]        Components of translation       
                                         vector.                         
41 - 70       String         text        Comment.                        

Details

* For structures not comprised of discrete molecules (e.g., infinite polysaccharide chains), the entry contains a fragment which can be built into the full structure by the simple translation vectors of TVECT records.

* A corresponding REMARK describing the structure must appear.

Verification/Validation/Value Authority Control

PDB applies the translation and checks the generated molecule.

Relationships to Other Record Types

A corresponding REMARK describing the structure must appear.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
TVECT    1   0.00000   0.00000  28.30000


9. Coordinate Section

The Coordinate Section contains the collection of atomic coordinates as well as the MODEL and ENDMDL records.


MODEL

Overview

The MODEL record specifies the model serial number when multiple structures are presented in a single coordinate entry, as is often the case with structures determined by NMR.

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                            
----------------------------------------------------------------------
 1 -  6       Record name    "MODEL "                                            
11 - 14       Integer        serial        Model serial number.                  

Details

* This record is used only when more than one model appears in an entry. Generally, it is employed only for NMR structures. The chemical connectivity should be the same for each model. ATOM, HETATM, SIGATM, SIGUIJ, ANISOU, and TER records for each model structure are interspersed as needed between MODEL and ENDMDL records.

* The numbering of models is sequential beginning with 1.

* If a collection contains more than 99,999 total atoms, then more than one entry must be made. In such a case the collection is divided between models (between an ENDMDL and the following MODEL record) and the model numbering is sequential throughout such a set of entries.

Verification/Validation/Value Authority Control

Entries with multiple structures in the EXPDTA record are checked for corresponding pairs of MODEL/ENDMDL records, and for consecutively numbered models.

Relationships to Other Record Types

Each MODEL must have a corresponding ENDMDL record.

In the case of an NMR entry the EXPDTA record states the number of model structures that are present in the individual entry.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL        1
ATOM      1  N   ALA     1      11.104   6.134  -6.504  1.00  0.00           N
ATOM      2  CA  ALA     1      11.639   6.071  -5.147  1.00  0.00           C
...
...
ATOM    293 1HG  GLU    18     -14.861  -4.847   0.361  1.00  0.00           H
ATOM    294 2HG  GLU    18     -13.518  -3.769   0.084  1.00  0.00           H
TER     295      GLU    18                                           
ENDMDL                                                              
MODEL        2                                                       
ATOM    296  N   ALA     1      10.883   6.779  -6.464  1.00  0.00           N
ATOM    297  CA  ALA     1      11.451   6.531  -5.142  1.00  0.00           C
...
...
ATOM    588 1HG  GLU    18     -13.363  -4.163  -2.372  1.00  0.00           H
ATOM    589 2HG  GLU    18     -12.634  -3.023  -3.475  1.00  0.00           H
TER     590      GLU    18                                          
ENDMDL


ATOM

Overview

The ATOM records present the atomic coordinates for standard residues. They also present the occupancy and temperature factor for each atom. Heterogen coordinates use the HETATM record type. The element symbol is always present on each ATOM record; segment identifier and charge are optional.

Record Format

COLUMNS        DATA TYPE       FIELD         DEFINITION                            
---------------------------------------------------------------------------------
 1 -  6        Record name     "ATOM  "                                            
 7 - 11        Integer         serial        Atom serial number.                   
13 - 16        Atom            name          Atom name.                            
17             Character       altLoc        Alternate location indicator.         
18 - 20        Residue name    resName       Residue name.                         
22             Character       chainID       Chain identifier.                     
23 - 26        Integer         resSeq        Residue sequence number.              
27             AChar           iCode         Code for insertion of residues.       
31 - 38        Real(8.3)       x             Orthogonal coordinates for X in       
                                             Angstroms.                       
39 - 46        Real(8.3)       y             Orthogonal coordinates for Y in       
                                             Angstroms.                            
47 - 54        Real(8.3)       z             Orthogonal coordinates for Z in       
                                             Angstroms.                            
55 - 60        Real(6.2)       occupancy     Occupancy.                            
61 - 66        Real(6.2)       tempFactor    Temperature factor.                   
73 - 76        LString(4)      segID         Segment identifier, left-justified.   
77 - 78        LString(2)      element       Element symbol, right-justified.      
79 - 80        LString(2)      charge        Charge on the atom.       

Details

* ATOM records for proteins are listed from amino to carboxyl terminus.

* Nucleic acid residues are listed from the 5' to the 3' terminus.

* No ordering is specified for polysaccharides.

* The list of ATOM records in a chain is terminated by a TER record.

* If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records.

* For more information on atom naming conventions, see Appendix 3, and for residue names, see Appendix 4 and the HET section of this document

* If an atom is provided in more than one position, then a non-blank alternate location indicator must be used as the alternate location indicator for each of the positions. Within a residue all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator.

* For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:

- In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry.
- In the case of a whole macromolecular chain, or significant portion of a chain, having alternate sites, the atoms for each alternate position are listed together. The two conformers are delineated by MODEL/ENDMDL records. In this case each MODEL must represent the entire molecular assemblage, including any heterogen group which is not necessarily disordered. Such is the case when DNA molecules are placed in UP and DOWN positions.
- In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together. The two lists are not separated by MODEL/ENDMDL as is done for macromolecular chains.

* Addition of atoms to side chains of standard residues are handled as follows:

The additional atoms (modifying group) are represented as a HET group which is assigned its own residue name. The chainID, sequence number, and insertion code assigned to the HET group is that of the standard residue to which it is attached.

* Chemical modifications of standard residue side chains by addition of new atoms are handled as follows:

- The new atoms are represented as a HET group. This group is assigned the chain name, sequence number, and insertion code of the standard residue that it modifies.
- The atoms comprising these het groups are listed as HETATM and are inserted in the ATOM list immediately after the TER record of the chain. These groups are listed in the same order as the standard residue to which they are bonded (i.e., from the N- to C-terminus for polypeptides and from the 5' to 3' end for nucleic acids).
- Modified standard residues and the modifying het group may be assigned the same SEGID to further describe the relationship between the groups. PDB will use this mechanism only if SEGID's were not assigned to these atoms for other purposes.
- Modified standard residues must have a corresponding MODRES record.

* The insertion code is commonly used in sequence numbering and is described here. In most cases, the amino acids that comprise a protein are numbered sequentially starting with 1. However, there are a number of situations that may give rise to different numbering schemes:

- Homologous proteins can exist in a number of different species. Depositors may use a residue numbering scheme in order to preserve the homology. The reference protein may be numbered sequentially starting with 1, then the homologous protein from another species aligned to it. If residues are not present in the homologous sequence, residue numbers may be skipped so that alignment can be preserved. If additional residues are present relative to the reference protein, they may have a letter, called an insertion code, appended to the sequence number. Negative numbers and zeros are permitted if they are needed to align the N-terminus.
     REFERENCE PROTEIN NUMBERING        HOMOLOGOUS PROTEIN NUMBERING        
     ---------------------------------------------------------------------
                 59                                  59                      
                 60                                  60                      
                 61                                                          
                 62                                  62                      

     REFERENCE PROTEIN NUMBERING         HOMOLOGOUS PROTEIN NUMBERING        
     ---------------------------------------------------------------------
                 85                                  85                      
                 86                                  86                      
                                                     86A                     
                                                     86B                     
                 87                                  87                      

- The numbering of a proenzyme may be used for the enzyme following cleavage.
- The molecule studied might be a portion of the whole protein. The residue numbering scheme could show the relationship to the intact protein.
- The protein might be a mutant with residues inserted and deleted. As above, the residue numbering of the native protein could be preserved by appropriate use of gaps in the numbering and/or insertion codes.
- The nucleic acid community generally numbers structures sequentially. For double-stranded nucleic acids, entries usually use two different chain identifiers. For example, an octameric duplex would be numbered 1 - 8 for chain A, and 9 - 16 for chain B.

* If the depositor provides the data, then the isotropic B value is given for the temperature factor.

* If there is no isotropic B value from the depositor, but there is an ANISOU record with anisotropic temperature factors, then the B equivalent is stored in the tempFactor field, as calculated by:

B(eq) = 8pi**2{1/3[U(1,1) + U(2,2) + U(3,3)]}
- This will obviate the need to check if ANISOU records are present before interpreting the contents of the temperature factor field.
- In some previously released PDB entries with anisotropic temperature factors provided as ANISOU records, the temperature factor field of the corresponding ATOM or HETATM record contained the equivalent U-isotropic [U(eq)] which is calculated by:
U(eq) = 1/3[U(1,1) + U(2,2) + U(3,3)] x 10**-4

* If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.

* In some entries, the occupancy and temperature factor fields are used for other quantities. In these cases, an explanation is provided in the remarks.

* Columns 73 - 76 identify specific segments of the molecule. The segment id is a string of up to four (4) alphanumeric characters, left-justified, and may include a space, e.g., CH86, A 1, NASE. The segment itself may consist of a complete chain or a portion of a chain. The importance of this new field can be appreciated if one considers an antibody structure having two molecules in the asymmetric unit. Since each chain must have a unique chain identifier, the two heavy chains and two light chains cannot currently be labeled to indicate their nature. Segment id's of CH, VH1, VH2, VH3, CL, and VL would clearly identify regions of the chains and the relationship between them. Users of X-PLOR will be familiar with SEGID as used in the refinement application of X-PLOR.

* Columns 77 - 78 contain the atom's element symbol (as given in the periodic table), right-justified. This is especially needed because in some cases it has not been possible to follow the convention that columns 13 - 14 of the atom name contain the element symbol. The most common cases are:

- In large het groups it sometimes is not possible to follow the convention of having the first two characters be the chemical symbol and still use atom names that are meaningful to users. A example is nicotinamide adenine dinucleotide, atom names begin with an A or N, depending on which portion of the molecule they appear in, e.g., AC6 or NC6, AN1 or NN1.
- Hydrogen naming sometimes conflicts with IUPAC conventions. For example, a hydrogen named HG11 in columns 13 - 16 is differentiated from a mercury atom by the element symbol in columns 77 - 78. Columns 13 - 16 present a unique name for each atom.

* Columns 79 - 80 indicate any charge on the atom, e.g., 2+, 1-. In most cases these are blank.

Verification/Validation/Value Authority Control

PDB checks ATOM/HETATM records for PDB format, sequence information, and packing. The PDB reserves the right to return deposited coordinates to the author for transformation into PDB format.

PDB intends to verify the coordinates against the experimental structure factor data in the when available. Details on this will be forthcoming.

Relationships to Other Record Types

The ATOM records are compared to the corresponding sequence database. Residue discrepancies appear in the SEQADV record. Missing atoms are annotated in the remarks. HETATM records are formatted in the same way as ATOM records. The sequence implied by ATOM records must be identical to that given in SEQRES, with the exception that residues that have no coordinates, e.g., due to disorder, must appear in SEQRES. Remark 550 is used to describe the meaning assigned to any segment identifiers used.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM    145  N   VAL A  25      32.433  16.336  57.540  1.00 11.92      A1   N
ATOM    146  CA  VAL A  25      31.132  16.439  58.160  1.00 11.85      A1   C
ATOM    147  C   VAL A  25      30.447  15.105  58.363  1.00 12.34      A1   C
ATOM    148  O   VAL A  25      29.520  15.059  59.174  1.00 15.65      A1   O
ATOM    149  CB AVAL A  25      30.385  17.437  57.230  0.28 13.88      A1   C
ATOM    150  CB BVAL A  25      30.166  17.399  57.373  0.72 15.41      A1   C
ATOM    151  CG1AVAL A  25      28.870  17.401  57.336  0.28 12.64      A1   C
ATOM    152  CG1BVAL A  25      30.805  18.788  57.449  0.72 15.11      A1   C
ATOM    153  CG2AVAL A  25      30.835  18.826  57.661  0.28 13.58      A1   C
ATOM    154  CG2BVAL A  25      29.909  16.996  55.922  0.72 13.25      A1   C

Known Problems

Due to the ever-increasing size of protein structures in the PDB, the atom serial number field may soon need to be increased. An increase of one column will allow for cases where entries have more than 99,999 atoms. Only 5 digits are available for the atom serial number, but some structures have already been received with more that 99,999 atoms.

No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U).


SIGATM

Overview

The SIGATM records present the standard deviation of atomic parameters as they appear in ATOM and HETATM records.

Record Format

COLUMNS        DATA TYPE       FIELD         DEFINITION                            
-----------------------------------------------------------------------------------
 1 -  6        Record name     "SIGATM"                                            
 7 - 11        Integer         serial        Atom serial number.                   
13 - 16        Atom            name          Atom name.                            
17             Character       altLoc        Alternate location indicator.         
18 - 20        Residue name    resName       Residue name.                         
22             Character       chainID       Chain identifier.                     
23 - 26        Integer         resSeq        Residue sequence number.              
27             AChar           iCode         Insertion code.                       
31 - 38        Real(8.3)       sigX          Standard deviations of the stored     
                                             coordinates (Angstroms).              
39 - 46        Real(8.3)       sigY          Standard deviations of the stored     
                                             coordinates (Angstroms).              
47 - 54        Real(8.3)       sigZ          Standard deviations of the stored     
                                             coordinates (Angstroms).              
55 - 60        Real(6.2)       sigOcc        Standard deviation of occupancy.      
61 - 66        Real(6.2)       sigTemp       Standard deviation of temperature     
                                             factor.                               
73 - 76        LString(4)      segID         Segment identifier, left-justified.   
77 - 78        LString(2)      element       Element symbol, right-justified.      
79 - 80        LString(2)      charge        Charge on the atom.       

Details

* Columns 7 - 27 and 73 - 80 are identical to the corresponding ATOM/HETATM record.

* Each SIGATM record immediately follows the corresponding ATOM/HETATM record.

* SIGATM is provided only for ATOM/HETATM records for which values are supplied by the depositor and only when the value is not zero (0).

Verification/Validation/Value Authority Control

The depositor provides SIGATM records, PDB verifies their format.

Relationships to Other Record Types

SIGATM is related to the immediately preceding ATOM/HETATM record.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM    230  N   PRO    15      20.860  29.640  13.460  1.00 12.20           N
SIGATM  230  N   PRO    15       0.040   0.030   0.030  0.00  0.00           N
ATOM    231  CA  PRO    15      22.180  29.010  12.960  1.00 14.70           C
SIGATM  231  CA  PRO    15       0.060   0.040   0.050  0.00  0.00           C
ATOM    232  C   PRO    15      23.170  30.090  12.670  1.00 19.10           C
SIGATM  232  C   PRO    15       0.080   0.070   0.060  0.00  0.00           C
ATOM    233  O   PRO    15      24.360  29.860  12.670  1.00 17.50           O
SIGATM  233  O   PRO    15       0.040   0.030   0.030  0.00  0.00           O
ATOM    234  CB  PRO    15      21.710  28.220  11.640  1.00 17.70           C
SIGATM  234  CB  PRO    15       0.060   0.040   0.050  0.00  0.00           C
ATOM    235  CG  PRO    15      20.470  28.710  11.590  1.00 23.90           C
SIGATM  235  CG  PRO    15       0.080   0.060   0.060  0.00  0.00           C
ATOM    236  CD  PRO    15      19.640  29.320  12.660  1.00 15.50           C
SIGATM  236  CD  PRO    15       0.060   0.040   0.050  0.00  0.00           C
ATOM    237  HA  PRO    15      22.630  28.400  13.620  1.00 14.70           H
ATOM    238 1HB  PRO    15      22.240  28.540  10.860  1.00 17.70           H
ATOM    239 2HB  PRO    15      21.670  27.240  11.840  1.00 17.70           H
ATOM    240 1HG  PRO    15      20.360  29.240  10.740  1.00 23.90           H
ATOM    241 2HG  PRO    15      19.900  28.120  11.020  1.00 23.90           H
ATOM    242 1HD  PRO    15      19.230  30.160  12.320  1.00 15.50           H
ATOM    243 2HD  PRO    15      19.120  28.600  13.120  1.00 15.50           H


ANISOU

Overview

The ANISOU records present the anisotropic temperature factors.

Record Format

COLUMNS        DATA TYPE       FIELD         DEFINITION                  
----------------------------------------------------------------------
 1 -  6        Record name     "ANISOU"                                  
 7 - 11        Integer         serial        Atom serial number.         
13 - 16        Atom            name          Atom name.                  
17             Character       altLoc        Alternate location          
                                             indicator.                  
18 - 20        Residue name    resName       Residue name.               
22             Character       chainID       Chain identifier.           
23 - 26        Integer         resSeq        Residue sequence number.    
27             AChar           iCode         Insertion code.             
29 - 35        Integer         u[0][0]       U(1,1)                
36 - 42        Integer         u[1][1]       U(2,2)                
43 - 49        Integer         u[2][2]       U(3,3)                
50 - 56        Integer         u[0][1]       U(1,2)                
57 - 63        Integer         u[0][2]       U(1,3)                
64 - 70        Integer         u[1][2]       U(2,3)                
73 - 76        LString(4)      segID         Segment identifier, left-justified.
77 - 78        LString(2)      element       Element symbol, right-justified.
79 - 80        LString(2)      charge        Charge on the atom.       

Details

* Columns 7 - 27 and 73 - 80 are identical to the corresponding ATOM/HETATM record.

* The anisotropic temperature factors (columns 29 - 70) are scaled by a factor of 10**4 (Angstroms**2) and are presented as integers.

* The anisotropic temperature factors are stored in the same coordinate frame as the atomic coordinate records.

* ANISOU values are listed only if they have been provided by the depositor.

Verification/Validation/Value Authority Control

The depositor provides ANISOU records, PDB verifies their format.

Relationships to Other Record Types

The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic temperature factors as B(eq), as described in the ATOM and HETATM sections.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM    107  N   GLY    13      12.681  37.302 -25.211 1.000 15.56           N
ANISOU  107  N   GLY    13     2406   1892   1614    198    519   -328       N
ATOM    108  CA  GLY    13      11.982  37.996 -26.241 1.000 16.92           C
ANISOU  108  CA  GLY    13     2748   2004   1679    -21    155   -419       C
ATOM    109  C   GLY    13      11.678  39.447 -26.008 1.000 15.73           C
ANISOU  109  C   GLY    13     2555   1955   1468     87    357   -109       C
ATOM    110  O   GLY    13      11.444  40.201 -26.971 1.000 20.93           O
ANISOU  110  O   GLY    13     3837   2505   1611    164   -121    189       O
ATOM    111  N   ASN    14      11.608  39.863 -24.755 1.000 13.68           N
ANISOU  111  N   ASN    14     2059   1674   1462     27    244    -96       N


SIGUIJ

Overview

The SIGUIJ records present the standard deviations of anisotropic temperature factors scaled by a factor of 10**4 (Angstroms**2).

Record Format

COLUMNS         DATA TYPE         FIELD         DEFINITION                     
-------------------------------------------------------------------------------
 1 -  6         Record name       "SIGUIJ"                                     
 7 - 11         Integer           serial        Atom serial number.            
13 - 16         Atom              name          Atom name.                     
17              Character         altLoc        Alternate location indicator.  
18 - 20         Residue name      resName       Residue name.                  
22              Character         chainID       Chain identifier.              
23 - 26         Integer           resSeq        Residue sequence number.       
27              AChar             iCode         Insertion code.                
29 - 35         Integer           sig[1][1]     Sigma U(1,1)                   
36 - 42         Integer           sig[2][2]     Sigma U(2,2)                   
43 - 49         Integer           sig[3][3]     Sigma U(3,3)                   
50 - 56         Integer           sig[1][2]     Sigma U(1,2)                   
57 - 63         Integer           sig[1][3]     Sigma U(1,3)                   
64 - 70         Integer           sig[2][3]     Sigma U(2,3)                   
73 - 76        LString(4)      segID         Segment identifier, left-justified.
77 - 78        LString(2)      element       Element symbol, right-justified.   
79 - 80        LString(2)      charge        Charge on the atom.       

Details

* Columns 7 - 27 and 73 - 80 are identical to the corresponding ATOM/HETATM record.

* SIGUIJ are listed only if they have been provided by the depositor and only if they are not zero (0).

Verification/Validation/Value Authority Control

The depositor provides SIGUIJ records, PDB verifies their format.

Relationships to Other Record Types

The standard deviations for the anisotropic temperature factors are related to the corresponding ATOM/HETATM ANISOU temperature factors.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM    107  N   GLY    13      12.681  37.302 -25.211 1.000 15.56           N
ANISOU  107  N   GLY    13     2406   1892   1614    198    519   -328       N
SIGUIJ  107  N   GLY    13       10     10     10     10    10      10       N
ATOM    108  CA  GLY    13      11.982  37.996 -26.241 1.000 16.92           C
ANISOU  108  CA  GLY    13     2748   2004   1679    -21    155   -419       C
SIGUIJ  108  CA  GLY    13       10     10     10     10    10      10       C
ATOM    109  C   GLY    13      11.678  39.447 -26.008 1.000 15.73           C
ANISOU  109  C   GLY    13     2555   1955   1468     87    357   -109       C
SIGUIJ  109  C   GLY    13       10     10     10     10    10      10       C
ATOM    110  O   GLY    13      11.444  40.201 -26.971 1.000 20.93           O
ANISOU  110  O   GLY    13     3837   2505   1611    164   -121    189       O
SIGUIJ  110  O   GLY    13       10     10     10     10    10      10       O
ATOM    111  N   ASN    14      11.608  39.863 -24.755 1.000 13.68           N
ANISOU  111  N   ASN    14     2059   1674   1462     27    244    -96       N
SIGUIJ  111  N   ASN    14       10     10     10     10    10      10       N


TER

Overview

The TER record indicates the end of a list of ATOM/HETATM records for a chain.

Record Format

COLUMNS         DATA TYPE         FIELD        DEFINITION                  
-------------------------------------------------------------------------
 1 -  6         Record name       "TER   "                                 
 7 - 11         Integer           serial       Serial number.         
18 - 20         Residue name      resName      Residue name.               
22              Character         chainID      Chain identifier.           
23 - 26         Integer           resSeq       Residue sequence number.    
27              AChar             iCode        Insertion code.     

Details

* Every chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record.

* The TER records occur in the coordinate section of the entry, and indicate the last residue presented for each polypeptide and/or nucleic acid chain for which there are coordinates. For proteins, the residue defined on the TER record is the carboxy-terminal residue; for nucleic acids it is the 3'-terminal residue.

* For a cyclic molecule, the choice of termini is arbitrary.

* Terminal oxygen atoms are presented as OXT for proteins, and as O5T or O3T for nucleic acids.

* The TER record has the same residue name, chain identifier, sequence number and insertion code as the terminal residue. The serial number of the TER record is one number greater than the serial number of the ATOM/HETATM preceding the TER.

* For chains with gaps due to disorder, it is recommended that the C-terminus atoms be labelled O and OXT, and a REMARK explaining the ambiguity be provided.

Verification/Validation/Value Authority Control

TER must appear at the end carboxy or 3' of a chain. For proteins, there is usually a terminal oxygen, labeled OXT. The validation program checks for the occurrence of TER and OXT records.

Relationships to Other Record Types

The residue name appearing on the TER record must be the same as the residue name of the immediately preceding ATOM or non-water HETATM record.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM   4150  H   ALA A 431       8.674  16.036  12.858  1.00  0.00           H
TER    4151      ALA A 431
ATOM   1403  O   PRO P  22      12.701  33.564  15.827  1.09 18.03           O
ATOM   1404  CB  PRO P  22      13.512  32.617  18.642  1.09  9.32           C
ATOM   1405  CG  PRO P  22      12.828  33.382  19.740  1.09 12.23           C
ATOM   1406  CD  PRO P  22      12.324  34.603  18.985  1.09 11.47           C
HETATM 1407  CA  BLE P   1      14.625  32.240  14.151  1.09 16.76           C
HETATM 1408  CB  BLE P   1      15.610  33.091  13.297  1.09 16.56           C
HETATM 1409  CG  BLE P   1      15.558  34.629  13.373  1.09 14.27           C
HETATM 1410  CD1 BLE P   1      16.601  35.208  12.440  1.09 14.75           C
HETATM 1411  CD2 BLE P   1      14.209  35.160  12.930  1.09 15.60           C
HETATM 1412  N   BLE P   1      14.777  32.703  15.531  1.09 14.79           N
HETATM 1413  B   BLE P   1      14.921  30.655  14.194  1.09 15.56           B
HETATM 1414  O1  BLE P   1      14.852  30.178  12.832  1.09 16.10           O
HETATM 1415  O2  BLE P   1      13.775  30.147  14.862  1.09 20.95           O
TER    1416      BLE P   1                                            


HETATM

Overview

The HETATM records present the atomic coordinate records for atoms within "non-standard" groups. These records are used for water molecules and atoms presented in HET groups.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
--------------------------------------------------------------------------------
 1 -  6        Record name     "HETATM"                                          
 7 - 11        Integer         serial         Atom serial number.                
13 - 16        Atom            name           Atom name.                         
17             Character       altLoc         Alternate location indicator.      
18 - 20        Residue name    resName        Residue name.                      
22             Character       chainID        Chain identifier.                  
23 - 26        Integer         resSeq         Residue sequence number.           
27             AChar           iCode          Code for insertion of residues.    
31 - 38        Real(8.3)       x              Orthogonal coordinates for X.      
39 - 46        Real(8.3)       y              Orthogonal coordinates for Y.      
47 - 54        Real(8.3)       z              Orthogonal coordinates for Z.      
55 - 60        Real(6.2)       occupancy      Occupancy.                         
61 - 66        Real(6.2)       tempFactor     Temperature factor.                
73 - 76        LString(4)      segID          Segment identifier;                
                                              left-justified.                    
77 - 78        LString(2)      element        Element symbol; right-justified.  
79 - 80        LString(2)      charge         Charge on the atom.    

Details

* The x, y, z coordinates are in Angstrom units.

* Disordered solvents may be represented by the residue name DIS.

* No ordering is specified for polysaccharides.

* See the HET section of this document regarding naming of heterogens. See the HET dictionary for residue names, formulas, and CONECT records of the HET groups that have appeared so far in the PDB.

* For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:

- In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry.
- In the case of a whole macromolecular chain, or significant portion of a chain, having alternate sites, the atoms for each alternate position are listed together. The two conformers are delineated by MODEL/ENDMDL records. In this case each MODEL must represent the entire molecular assemblage, including any heterogen group which is not necessarily disordered. Such is the case when DNA molecules are placed in UP and DOWN positions.
- In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together. The two lists are not separated by MODEL/ENDMDL as is done for macromolecular chains.

* If the depositor provides the data, then the isotropic B value is given for the temperature factor.

* If there is no isotropic B value from the depositor, but there is an ANISOU record with anisotropic temperature factors, then the B equivalent is stored in the tempFactor field, as calculated by:

B(eq) = 8pi**2{1/3[U(1,1) + U(2,2) + U(3,3)]}
- This will obviate the need to check if ANISOU records are present before interpreting the contents of the temperature factor field.
- In some previously released PDB entries with anisotropic temperature factors provided as ANISOU records, the temperature factor field of the corresponding ATOM or HETATM record contained the equivalent U-isotropic [U(eq)] which is calculated by:
U(eq) = 1/3[U(1,1) + U(2,2) + U(3,3)] x 10**-4

* If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.

* In some entries, the occupancy and temperature factor fields are often used for other quantities. In these cases, an explanation is provided in the remarks.

* Insertion codes, segment id, and element naming are fully described in the ATOM section of this document.

Verification/Validation/Value Authority Control

PDB processing programs check ATOM/HETATM records for PDB format, sequence information, and packing. The PDB reserves the right to return deposited coordinates to the author for transformation into PDB format.

Relationships to Other Record Types

HETATM records must have corresponding HET, HETNAM, FORMUL and CONECT records, except for waters.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETATM 1357 MG    MG   168       4.669  34.118  19.123  1.00  3.16          MG2+
HETATM 3835 FE   HEM     1      17.140   3.115  15.066  1.00 14.14          FE3+


ENDMDL

Overview

The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.

Record Format

COLUMNS         DATA TYPE        FIELD           DEFINITION       
------------------------------------------------------------------
 1 -  6         Record name      "ENDMDL"                         

Details

* MODEL/ENDMDL records are used only when more than one structure is presented in the entry, as is often the case with NMR entries.

* All the models in a multi-model entry must represent the same structure.

* Every MODEL record has an associated ENDMDL record.

Verification/Validation/Value Authority Control

Entries with multiple structures in the EXPDTA record are checked for corresponding pairs of MODEL/ENDMDL records, and for consecutively numbered models.

Relationships to Other Record Types

There must be a corresponding MODEL record.

In the case of an NMR entry the EXPDTA record states the number of model structures that are present in the individual entry.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
...
...
ATOM  14550 1HG  GLU   122     -14.364  14.787 -14.258  1.00  0.00           H
ATOM  14551 2HG  GLU   122     -13.794  13.738 -12.961  1.00  0.00           H
TER   14552      GLU   122                                             
ENDMDL                                                                 
MODEL        9                                                         
ATOM  14553  N   SER     1     -28.280   1.567  12.004  1.00  0.00           N
ATOM  14554  CA  SER     1     -27.749   0.392  11.256  1.00  0.00           C
...
...
ATOM  16369 1HG  GLU   122      -3.757  18.546  -8.439  1.00  0.00           H
ATOM  16370 2HG  GLU   122      -3.066  17.166  -7.584  1.00  0.00           H
TER   16371      GLU   122                                             
ENDMDL                                                                 
MODEL       10                                                         
ATOM  16372  N   SER     1     -22.285   7.041  10.003  1.00  0.00           N
ATOM  16373  CA  SER     1     -23.026   6.872   8.720  1.00  0.00           C
...
...
ATOM  18188 1HG  GLU   122      -1.467  18.282 -17.144  1.00  0.00           H
ATOM  18189 2HG  GLU   122      -2.711  18.067 -15.913  1.00  0.00           H
TER   18190      GLU   122                                             
ENDMDL


10. Connectivity Section

This section provides information on chemical connectivity. LINK, HYDBND, SLTBRG, and CISPEP are found in the Connectivity Annotation section.


CONECT

Overview

The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues (see Appendix 4 for the list of standard residues). These records are generated by the PDB.

Record Format

COLUMNS         DATA TYPE        FIELD           DEFINITION                      
---------------------------------------------------------------------------------
 1 -  6         Record name      "CONECT"                                        
 7 - 11         Integer          serial          Atom serial number              
12 - 16         Integer          serial          Serial number of bonded atom    
17 - 21         Integer          serial          Serial number of bonded atom    
22 - 26         Integer          serial          Serial number of bonded atom    
27 - 31         Integer          serial          Serial number of bonded atom    
32 - 36         Integer          serial          Serial number of hydrogen bonded 
                                                 atom    
37 - 41         Integer          serial          Serial number of hydrogen bonded 
                                                 atom    
42 - 46         Integer          serial          Serial number of salt bridged    
                                                 atom    
47 - 51         Integer          serial          Serial number of hydrogen bonded 
                                                 atom    
52 - 56         Integer          serial          Serial number of hydrogen bonded 
                                                 atom    
57 - 61         Integer          serial          Serial number of salt bridged    
                                                 atom    

Details

* Intra-residue connectivity within non-standard (HET) residues (excluding water) is presented on the CONECT records.

* Inter-residue connectivity of HET groups to standard groups (including water) or to other HET groups are represented on the CONECT records.

* Disulfide bridges specified in the SSBOND records have corresponding CONECT records.

* Hydrogen bonds and salt bridges have CONECT records.

* No differentiation is made between donor and acceptor for hydrogen bonds.

* No differentiation is made between atoms with excess negative or positive charge.

* Atoms specified in the connectivity are presented by their serial numbers as found in the entry.

* All atoms connected to the atom with serial number in columns 7 - 11 are listed in the remaining fields of the record.

* If more than four fields are required for non-hydrogen and nonsalt-bridge bonds, a second CONECT record with the same atom serial number in columns 7 - 11 will be used.

* These CONECT records occur in increasing order of the atom serial numbers they carry in columns 7 - 11. The target-atom serial numbers carried on these records also occur in increasing order.

* The connectivity list given here is redundant in that each bond indicated is given twice, once with each of the two atoms involved specified in columns 7 - 11.

* For nucleic acids, Watson-Crick hydrogen bonds between bases may be listed, but this is optional.

* For hydrogen bonds, when the hydrogen atom is present in the coordinates, PDB generates a CONECT record between the hydrogen atom and its acceptor atom.

* For NMR entries, CONECT records for all models are generated describing heterogen connectivity and others for LINK records.

Verification/Validation/Value Authority Control

Connectivity is checked for unusual bond lengths.

Relationships to Other Record Types

CONECT records must be present in an entry that contains either non-standard groups or disulfide bonds.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
CONECT 1179  746 1184 1195 1203                    
CONECT 1179 1211 1222                              
CONECT 1021  544 1017 1020 1022 1211 1222      1311

Known Problems

Only five digits are available for the atom serial number, but some structures have already been received with more that 99,999 atoms. Changing the field length would make earlier entries incorrect.

CONECTs to atoms whose coordinates are not in the entry (e.g., symmetry-generated) are not given.



11. Bookkeeping Section

The Bookkeeping Section provides some final information about the file itself.


MASTER

Overview

The MASTER record is a control record for bookkeeping. It lists the number of lines in the coordinate entry or file for selected record types.

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                             
----------------------------------------------------------------------------------
 1 -  6       Record name    "MASTER"                                             
11 - 15       Integer        numRemark     Number of REMARK records               
16 - 20       Integer        "0"                                                  
21 - 25       Integer        numHet        Number of HET records                  
26 - 30       Integer        numHelix      Number of HELIX records                
31 - 35       Integer        numSheet      Number of SHEET records                
36 - 40       Integer        numTurn       Number of TURN records                 
41 - 45       Integer        numSite       Number of SITE records                 
46 - 50       Integer        numXform      Number of coordinate transformation    
                                           records (ORIGX+SCALE+MTRIX)            
51 - 55       Integer        numCoord      Number of atomic coordinate records    
                                           (ATOM+HETATM)                          
56 - 60       Integer        numTer        Number of TER records                  
61 - 65       Integer        numConect     Number of CONECT records               
66 - 70       Integer        numSeq        Number of SEQRES records               

Details

* MASTER gives checksums of the number of records in the entry, for selected record types.

Verification/Validation/Value Authority Control

The MASTER line is generated by the PDB.

Relationships to Other Record Types

MASTER presents a checksum of the lines present for each of the record types listed above.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
MASTER       40    0    0    0    0    0    0    6 2930    2    0   29


END

Overview

The END record marks the end of the PDB file.

Record Format

COLUMNS       DATA TYPE      FIELD     DEFINITION      
-------------------------------------------------------
 1 -  6       Record name    "END   "                  

Details

* END is the final record of a coordinate entry.

Verification/Validation/Value Authority Control

END must appear in every coordinate entry.

Relationships to Other Record Types

This is the final record in the entry.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
END

Protein Data Bank Contents Guide:

Atomic Coordinate Entry Format Description:

Appendices


Appendix 1: Symmetry Operations

The data type SymOP is used to succinctly describe crystallographic symmetry operations that may be performed on ATOM/HETATM coordinates. Symmetry operators applicable to a given entry are presented in REMARK 290. Each operator is assigned a serial number. The SymOP is a number of up to six (6) digits that indicates the serial number of the symmetry operator and the cell translations along the x, y, and z axes.

The SymOP data type is of the form nnnMMM where 'n' is the serial number of the symmetry operator, and 'MMM' is the concatenated cell translations along x, y, z with respect to the base number 555. Symmetry operators listed in REMARK 290 operate on orthogonal crystallographic coordinates that appear in the entry..

The FORTRAN I3 I3 format statement can be used to interpret nnnMMM.

As an example, the SymOP 2456 indicates that the second symmetry operation as listed in REMARK 290 is applied with translation of -1 on x, and +1 on z. A program will be made available shortly that converts SymOP data into transformations that operate in the coordinate frame used in the entry.

The SymOP data type is used in SSBOND, LINK, HYDBND, SLTBRG and REMARKs.

Template

1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 290                                                            
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                  
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21             
REMARK 290                                                            
REMARK 290      SYMOP   SYMMETRY                                      
REMARK 290     NNNMMM   OPERATOR                                      
REMARK 290       1555   X,Y,Z                                         
REMARK 290       2555   1/2-X,-Y,1/2+Z                                
REMARK 290       3555   -X,1/2+Y,1/2-Z                                
REMARK 290       4555   1/2+X,1/2-Y,-Z                                
REMARK 290                                                            
REMARK 290     WHERE NNN -> OPERATOR NUMBER                           
REMARK 290           MMM -> TRANSLATION VECTOR                        
REMARK 290                                                            
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                  
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM   
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY      
REMARK 290 RELATED MOLECULES. 
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000  
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       36.30027  
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       59.50256  
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       59.50256  
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       36.30027  
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000 
REMARK 290                                                            
REMARK 290 REMARK: NULL                                               


Appendix 2: Coordinate Systems and Transformations

The coordinates distributed by the Protein Data Bank give the atomic positions measured in Angstroms along three orthogonal directions. Unless otherwise specified, the default axial system detailed below is assumed.

If a, b, c describe the crystallographic cell edges and A, B, C are unit vectors in the default orthogonal Angstrom system, then the following apply.

A, B, C and a, b, c have the same origin.
A is parallel to a.
B is parallel to (a X b) X A (cross product between C and A).
C is parallel to a X b (i.e., c*) (cross product between a and b).

The matrix which pre-multiplies the column vector of the fractional crystallographic coordinates to yield the distributed coordinates in the A, B, C system is:

      a   b(cos(gamma))   c(cos(beta))                                      
      0   b(sin(gamma))   c(cos(alpha) - cos(beta) cos(gamma)) / sin(gamma)
      0   0               V/(ab sin(gamma))                                 

V = abc(1 - cos**2(alpha) - cos**2(beta) - cos**2(gamma) + 2(cos(alpha) cos(beta) cos(gamma)))**1/2

The distributed entry will contain the following records.

ORIGX - transformation from the distributed to the submitted coordinates.
SCALE - transformation from the distributed to the fractional coordinates.

Appendix 3: Atom Names

Amino Acids

The following rules are used in assigning atom names.

* Greek letter remoteness codes are transliterated as follows: alpha = A, beta = B, gamma = G, delta = D, epsilon = E, zeta = Z, eta = H, etc.

* Atoms for which some ambiguity exists in the crystallographic results are designated A. This usually applies only to the terminal atoms of asparagine and glutamine and to the ring atoms of histidine.

* The extra oxygen atom of the carboxy terminal amino acid is designated OXT.

* Six characters (columns) are reserved for atom names, assigned as follows.

   COLUMN     VALUE                                 
   -----------------------------------------------------------------------
   13 - 14    Chemical symbol - right justified, except for hydrogen atoms
   15         Remoteness indicator (alphabetic)      
   16         Branch designator (numeric)            
   77 - 78    Element symbol, right-justified

* Columns 73 - 76 identify specific segments of the molecule. The segment may consist of a complete chain or a portion of a chain. The importance of this new field can be appreciated if one considers an antibody structure having two molecules in the asymmetric unit. Since each chain must have a unique chain identifier, the two heavy chains and two light chains cannot currently be labeled to indicate their nature. Segment id's of CH, VH1, VH2, VH3, CL, and VL would clearly identify regions of the chains and the relationship between them. Users of X-PLOR will be familiar with SEGID as used in the refinement application of X-PLOR.

See the ATOM record for more details on atom naming.

Nucleic Acids

Atom names employed for polynucleotides generally follow the precedent set for mononucleotides. The following points should be noted.

* The asterisk (*) is used in place of the prime character (') for naming atoms of the sugar group. The prime was avoided historically because of non-uniformity of its external representation.

* The ring oxygen of the ribose is denoted O4 rather than O1.

* The extra oxygen atom at the free 5' and 3' termini are designated O5T and O3T, respectively.


Appendix 4: Standard Residue Names and Abbreviations

Note that there will be a change to what are considered standard groups due to the adoption of the new PDB Het Group Dictionary. Only the twenty common amino acids and five nucleic acids plus inosine will be treated as "standard" with all others being treated as modified residues to be described by MODRES records.

No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U, I).

Amino Acids

RESIDUE                     ABBREVIATION                SYNONYM                 
-----------------------------------------------------------------------------
Alanine                     ALA                         A                       
Arginine                    ARG                         R                       
Asparagine                  ASN                         N                       
Aspartic acid               ASP                         D                       
ASP/ASN ambiguous           ASX                         B                       
Cysteine                    CYS                         C                       
Glutamine                   GLN                         Q                       
Glutamic acid               GLU                         E                       
GLU/GLN ambiguous           GLX                         Z                       
Glycine                     GLY                         G                       
Histidine                   HIS                         H                       
Isoleucine                  ILE                         I                       
Leucine                     LEU                         L                       
Lysine                      LYS                         K                       
Methionine                  MET                         M                       
Phenylalanine               PHE                         F                       
Proline                     PRO                         P                       
Serine                      SER                         S                       
Threonine                   THR                         T                       
Tryptophan                  TRP                         W                       
Tyrosine                    TYR                         Y                       
Unknown                     UNK                                                 
Valine                      VAL                         V                       

Nucleic Acids

RESIDUE                                  ABBREVIATION                           
-----------------------------------------------------------------------
Adenosine                                  A                                     
Modified adenosine                        +A                                     
Cytidine                                   C                                     
Modified cytidine                         +C                                     
Guanosine                                  G                                     
Modified guanosine                        +G                                     
Inosine                                    I                                     
Modified inosine                          +I                                     
Thymidine                                  T                                     
Modified thymidine                        +T                                     
Uridine                                    U                                     
Modified uridine                          +U                                     
Unknown                                  UNK                                     

Remarks 103 and 104 are included when an entry contains inosine.


Appendix 5: Formulas and Molecular Weights for Standard Residues

These weights and formulas correspond to the unpolymerized state of the component. The atoms of one water molecule are eliminated for each two components joined.

Amino Acids

NAME                    CODE           FORMULA                 MOL. WT.          
-----------------------------------------------------------------------------
Alanine                 ALA            C3 H7 N1 O2             89.09             
Arginine                ARG            C6 H14 N4 O2            174.20            
Asparagine              ASN            C4 H8 N2 O3             132.12            
Aspartic acid           ASP            C4 H7 N1 O4             133.10            
ASP/ASN ambiguous       ASX            C4 H71/2 N11/2 O31/2    132.61            
Cysteine                CYS            C3 H7 N1 O2 S1          121.15            
Glutamine               GLN            C5 H10 N2 O3            146.15            
Glutamic acid           GLU            C5 H9 N1 O4             147.13            
GLU/GLN ambiguous       GLX            C5 H91/2 N11/2 O31/2    146.64            
Glycine                 GLY            C2 H5 N1 O2             75.07             
Histidine               HIS            C6 H9 N3 O2             155.16            
Isoleucine              ILE            C6 H13 N1 O2            131.17            
Leucine                 LEU            C6 H13 N1 O2            131.17            
Lysine                  LYS            C6 H14 N2 O2            146.19            
Methionine              MET            C5 H11 N1 O2 S1         149.21            
Phenylalanine           PHE            C9 H11 N1 O2            165.19            
Proline                 PRO            C5 H9 N1 O2             115.13            
Serine                  SER            C3 H7 N1 O3             105.09           
Threonine               THR            C4 H9 N1 O3             119.12           
Tryptophan              TRP            C11 H12 N2 O2           204.23            
Tyrosine                TYR            C9 H11 N1 O3            181.19            
Valine                  VAL            C5 H11 N1 O2            117.15            
Undetermined            UNK            C5 H6 N1 O3             128.16            

Nucleotides

NAME                    CODE           FORMULA                 MOL. WT.     
------------------------------------------------------------------------------
Adenosine               A              C10 H14 N5 O7 P1        347.22 
Cytidine                C              C9 H14 N3 O8 P1         323.20 
Guanosine               G              C10 H14 N5 O8 P1        363.22 
Inosine                 I              C10 H13 N4 08 P1        348.21
Thymidine               T              C10 H15 N2 08 P1        322.21
Uridine                 U              C9 H13 N2 09 P1         324.18


Appendix 6: Field Formats

(This information is repeated from the Introduction.)

Each record type is presented in a table which contains the division of the records into fields by column number, defined data type, field name or a quoted string which must appear in the field, and field definition. Any column not specified must be left blank.

Each field contains an identified data type which can be validated by a program. These are:

DATA TYPE          DESCRIPTION                                                   
---------------------------------------------------------------------------------
AChar              An alphabetic character (A-Z, a-z).    
Atom               Atom name which follow the naming rules in Appendix 3.        
Character          Any non-control character in the ASCII character set or a     
                   space.                                                       
Continuation       A two-character field that is either blank (for the first     
                   record of a set) or contains a two digit number             
                   right-justified and blank-filled which counts continuation  
                   records starting with 2. The continuation number must be  
                   followed by a blank.                                        
Date               A 9 character string in the form dd-mmm-yy where DD is the    
                   day of the month, zero-filled on the left (e.g., 04); MMM is
                   the common English 3-letter abbreviation of the month; and  
                   YY is a year in the 20th century.  This must represent a    
                   valid date.                                                  
IDcode             A PDB identification code which consists of 4 characters,     
                   the first of which is a digit in the range 0 - 9; the       
                   remaining 3 are alpha-numeric, and letters are upper case   
                   only.  Entries with a 0 as the first character do not       
                   contain coordinate data.                                     
Integer            Right-justified blank-filled integer value.                   
Token              A sequence of non-space characters followed by a colon and a  
                   space.                                                      
List               A String that is composed of text separated with commas.      
LString            A literal string of characters.  All spacing is significant   
                   and must be preserved.                                      
LString(n)         An LString with exactly n characters.                         
Real(n,m)          Real (floating point) number in the FORTRAN format Fn.m.      
Record name        The name of the record: 6 characters, left-justified and      
                   blank-filled.                                               
Residue name       One of the standard amino acid or nucleic acids, as listed    
                   below, or the non-standard group designation as defined in  
                   the HET dictionary. Field is right-justified.               
SList              A String that is composed of text separated with semi-colons. 
Specification      A String composed of a token and its associated value         
                   separated by a colon.                                      
Specification      A sequence of Specifications, separated by semi-colons.       
list                                                                           
String             A sequence of characters.  These characters may have          
                   arbitrary spacing, but should be interpreted as directed    
                   below.                                                      
String(n)          A String with exactly n characters.                           
SymOP              An integer field of from 4 to 6 digits, right-justified, of   
                   the form nnnMMM where nnn is the symmetry operator number   
                   and MMM is the translation vector. See details in Appendix 1.

To interpret a String, concatenate the contents of all continued fields together, collapse all sequences of multiple blanks to a single blank, and remove any leading and trailing blanks. This permits very long strings to be properly reconstructed.


Appendix 7: Order of Records

(This information is repeated from the Introduction.)

All records in a PDB coordinate entry must appear in a defined order. Mandatory record types are present in all entries. When mandatory data are not provided, the record name must appear in the entry with a NULL indicator. Optional items become mandatory when certain conditions exist. Record order and existence are described in the following table:

RECORD TYPE                 EXISTENCE      CONDITIONS IF OPTIONAL                
---------------------------------------------------------------------------------
HEADER                      Mandatory                                            
OBSLTE                      Optional       Mandatory in withdrawn entries.       
TITLE                       Mandatory                                            
CAVEAT                      Optional       Mandatory if structure is deemed      
                                           incorrect by an outside editorial   
                                           board.                               
COMPND                      Mandatory                                            
SOURCE                      Mandatory                                            
KEYWDS                      Mandatory                                            
EXPDTA                      Mandatory                                            
AUTHOR                      Mandatory                                            
REVDAT                      Mandatory                                            
SPRSDE                      Optional       Mandatory if a replacement entry.     
JRNL                        Optional       Mandatory if a publication describes  
                                           the experiment.                     
REMARK 1                    Optional                                             
REMARK 2                    Mandatory                                            
REMARK 3                    Mandatory                                            
REMARK N                    Optional                                           
DBREF                       Optional       Mandatory for each peptide chain with 
                                           a length greater than ten (10)      
                                           residues, and for nucleic acid.      
                                           entries that exist in the Nucleic   
                                           Acid Database (NDB).                 
SEQADV                      Optional       Mandatory if sequence conflict exists.
SEQRES                      Optional       Mandatory if ATOM records exist.      
MODRES                      Optional       Mandatory if modified group exists    
                                           within the coordinates.              
HET                         Optional       Mandatory if non-standard group other 
                                           than water appears in the entry.     
HETNAM                      Optional       Mandatory if non-standard group other 
                                           than water appears in the entry.      
HETSYN                      Optional                                     
FORMUL                      Optional       Mandatory if non-standard group or    
                                           water appears.                       
HELIX                       Optional                      
SHEET                       Optional                       
TURN                        Optional                         
SSBOND                      Optional       Mandatory if disulfide bond is present.
LINK                        Optional                                             
HYDBND                      Optional                                             
SLTBRG                      Optional                                             
CISPEP                      Optional                                             
SITE                        Optional                                             
CRYST1                      Mandatory                                             
ORIGX1 ORIGX2 ORIGX3        Mandatory                                             
SCALE1 SCALE2 SCALE3        Mandatory                                             
MTRIX1 MTRIX2 MTRIX3        Optional       Mandatory if the complete asymmetric   
                                           unit must be generated from the given
                                           coordinates using                    
                                           non-crystallographic symmetry.        
TVECT                       Optional                        
MODEL                       Optional       Mandatory if more than one model    
                                           is present in the entry.              
ATOM                        Optional       Mandatory if standard residues exist.  
SIGATM                      Optional                                              
ANISOU                      Optional                                              
SIGUIJ                      Optional                                              
TER                         Optional       Mandatory if ATOM records exist.       
HETATM                      Optional       Mandatory if non-standard group 
                                           appears.
ENDMDL                      Optional       Mandatory if MODEL appears.            
CONECT                      Optional       Mandatory if non-standard group        
                                           appears.                              
MASTER                      Mandatory                                             
END                         Mandatory                                             

Note that a PDB file existing outside of the PDB official release may contain locally-defined records beginning with "USER". The PDB reserves the right to add new record types (not beginning with "USER"), so programs which read PDB entries should be prepared to read (and ignore) other record types. PDB will follow standard procedures whenever format changes are proposed.

Sections of an Entry

The following table lists the various sections of a PDB coordinate entry and the records comprising them:

SECTION              DESCRIPTION                    RECORD TYPE                   
----------------------------------------------------------------------------------
Title                Summary descriptive remarks    HEADER, OBSLTE, TITLE,        
                                                    CAVEAT, COMPND, SOURCE,       
                                                    KEYWDS, EXPDTA, AUTHOR,       
                                                    REVDAT, SPRSDE, JRNL          
Remark               Bibliography, refinement,      REMARKs 1, 2, 3 and others    
                     annotations                                           
Primary structure    Peptide and/or nucleotide      MODRES, DBREF, SEQADV, SEQRES 
                     sequence and the                                           
                     relationship between the                                
                     PDB sequence and that                                  
                     found in the sequence                                   
                     database(s)                                             
Heterogen            Description of non-standard    HET, HETNAM, HETSYN, FORMUL   
                     groups                                                     
Secondary structure  Description of secondary       HELIX, SHEET, TURN            
                     structure                                                  
Connectivity         Chemical connectivity          SSBOND, LINK, HYDBND,         
annotation                                          SLTBRG, CISPEP                
Miscellaneous        Features within the            SITE                   
features             macromolecule                                              
Crystallographic     Description of the             CRYST1                        
                     crystallographic cell                                      
Coordinate           Coordinate transformation      ORIGXn, SCALEn, MTRIXn, TVECT 
transformation       operators                                                  
Coordinate           Atomic coordinate data         MODEL, ATOM, SIGATM, ANISOU,  
                                                    SIGUIJ, TER, HETATM, ENDMDL   
Connectivity         Chemical connectivity          CONECT
Bookkeeping          Summary information,           MASTER, END                   
                     end-of-file marker