PDB FORMAT: (CCP4: Formats)

NAME

DESCRIPTION

CCP4 uses a subset of the PDB format for holding information on atomic coordinates and other model information. The full format description can be found at the wwPDB site.

CCP4 programs also use the PDB format for holding other information, such as lists of peaks in maps, Patterson vectors, etc.

Authors of this document: John W. Campbell, Adam C. Ralph and Martyn Winn.

CONTENTS

1. INTRODUCTION
2. FORMAT OF THE 'ATOM/HETATM' CARDS
3. FORMAT OF THE 'TER' CARDS
4. FORMAT OF THE 'CRYST1' CARD
5. FORMAT OF THE 'SCALE' CARDS
6. FORMAT OF THE 'ANISOU' CARD
7. STANDARD RESIDUE NAMES
8. ATOM IDENTIFIERS FOR AMINO ACIDS
9. REFERENCES

INTRODUCTION

The standard coordinate data file format adopted for the CCP4 protein crystallography program suite is that of the Protein Data Bank (ref. 1). The programs will handle either complete files or files containing only a subset of the types of record which may be present in a complete file. In particular, the records containing the coordinate data (ATOM, HETATM and ANISOU records) are of interest. Their structures and those of the TER, CRYST1 and SCALE records, which are also used by the file handling subroutines described in rwbrook.html, are outlined below. The PDB format defines a standard setting of orthogonal axes with respect to the crystallographic axes and this has been adopted as the standard for the CCP. The standard set of orthogonal axes XO, YO and ZO is defined as follows:

   XO // a
   YO // c* × a
   ZO // c*

Within a PDB format file, however, coordinates may be held with respect to other sets of axes. If files are in a non-standard axis setting then the CRYST1 or SCALE cards must be present. A complete description of the file format is available from the wwPDB but some selected features, relevant to the handling of the coordinate data are described below. In general terms it may be noted that the format is basically a card image format with fixed length 80 byte records.

FORMAT OF THE 'ATOM/HETATM' CARDS

The format of an 'ATOM' card or 'HETATM' card is as follows:

Cols.  1-6    Record name "ATOM  " or "HETATM"
       7-11   Atom serial number                   (see note i)
      13-14   Chemical symbol (right justified)  )
      15      Remoteness indicator               ) (see note ii)
      16      Branch designator                  )
      17      Alternate location indicator         (see note iii)
      18-20   Residue name                         (see note iv)
      21      Reserved                   )
      22      Chain identifier           )
                                         )         (see note v)
      23-26   Residue sequence number    )
      27      Code for inserting residue )
      31-38   X   )
      39-46   Y   ) Orthogonal Angstrom coordinates
      47-54   Z   )
      55-60   Occupancy
      61-66   Isotropic B-factor
      73-76   Segment identifier, left justified (used by XPLOR)
      77-78   Element symbol, right justified )
                                              )    (see note vi)
      79-80   Charge on atom                  )

Typical format:  
          (6A1,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,6X,2A4)

Notes:
1. Residues occur in order of their sequence numbers which always increase starting from the N-terminal residue. Within each residue, the order of the atoms does not matter in general. However, there is a standard order defined by the PDB standard. If the residue sequence is known, certain serial numbers may be omitted to allow for the future insertion of any missing atoms. If the sequence is not reliably known these serial numbers are simply ordinals.
2. The atom names are described in below.
3. Alternate locations for atoms may be denoted by A, B, C etc. here.
4. The standard residue names are given in paragraph 6 below.
5. The sequence identifier is a composite field made up as follows:

   Cols. 21      Reserved for future expansion
         22      Chain identifier, e.g. A for Haemoglobin 
                 alpha chain
         23-26   Residue sequence number
         27      Code for insertions of residues, 
                 e.g. 66A, 66B etc.
   

FORMAT OF THE 'TER' CARDS

'TER' cards are used to indicate chain terminations. They are placed at the appropriate positions within the atom cards. The format of a 'TER' card is as follows:

Cols.  1-3    Record name "TER"
      7-11    Serial number
      18-20   Residue name
      21-27   Sequence identifier (see description of 'ATOM' 
                                   cards above)

Typical format:  (6A1,I5,6X,A3,1X,A1,I4,A1)

FORMAT OF THE 'CRYST1' CARD

This card holds the cell parameters and has the following format

Cols.  1-6    Record name "CRYST1"
      7-15    a (Å)
     16-24    b (Å)
     25-33    c (Å)
     34-40    alpha (°)
     41-47    beta  (°)
     48-54    gamma (°)
     56-66    Space group symbol, left justified (not used)
     67-70    Z    (not used)

Typical Format:  (6A1,3F9.3,3F7.2,1X,11A1,I4)

FORMAT OF THE 'SCALE' CARDS

These cards hold the matrix for transforming the stored orthogonal Angstrom coordinates to fractional crystallographic coordinates. Three cards are required. 'S' is the rotation matrix and 'U' is the translation matrix. The format of the cards is as follows.

Cols.  1-6      SCALE1     SCALE2     SCALE3
     11-20      S11        S21        S31
     21-30      S12        S22        S32
     31-40      S13        S23        S33
     46-55      U1         U2         U3

Typical Format:  (6A1,4X,3F10.6,5X,F10.5)

To remind you:

If you have a PDB file

,

where

,

the matrix at the head of a PDB file, i.e.

.

Therefore, extending Scalei to ScaleiExt so that the 4×4 inverse matrix can be generated^{footnote ¶}

,

.

The programs COORDCONV, VECTORS and HAVECS will all convert (various formats of) fractional coordinates to orthogonal ones. HAVECS's PHARE input type corresponds to MLPHARE's output coordinate format.

Footnote ¶: The extension line ([ 0.00  0.00  0.00  1.00]) is necessary to cope with [Scale₁₄,Scale₂₄,Scale₃₄], the translation component of the transformation.

FORMAT OF THE 'ANISOU' CARD

This card holds information about the anisotropic temperature factors for a particular atom, if they are refined. Note that columns 7-27 and 73-80 are the same as the corresponding atom card. The temperature factors are multiplied by a factor of 10**4, held as integers and represent orthogonal Us. The axis system they are based on is the same as that on which the orthogonal co-ordinates are based. The format follows:

Cols:   1-6    Record name "ANISOU"                                  
       7-11    Atom serial number.         
      13-16    Atom name
         17    Alternate location indicator. 
      18-20    Residue name
         22    Chain identifier.
      23-26    Residue sequence number.    
         27    Insertion code. 
      29-35    U(1,1)
      36-42    U(2,2)
      43-49    U(3,3)
      50-56    U(1,2)
      57-63    U(1,3)
      64-70    U(2,3)
      73-76    Segment identifier, left-justified.
      77-78    Element symbol, right-justified.
      79-80    Charge on the atom.       

The isotropic temperature factor defined in the ATOM card is defined as:

    Biso = 8pi² × (U(1,1) + U(2,2) + U(3,3))/3

STANDARD RESIDUE NAMES

The residue abbreviations for the amino acids conform to the IUPAC-IUB rules (ref. 2). Non-standard residues are given a three character abbreviation chosen by the user. The amino acids and their abbreviations are given in the table below.

Residue	Abb.	Residue	Abb.
Acidic unknown	ACD	Homoserine	HSE
Acetyl	ACE	Hydroxyproline	HYP
Alanine	ALA	Hydroxylysine	HYL
beta-Alanine	ALB	Isoleucine	ILE
Aliphatic unknown	ALI	Leucine	LEU
gamma-Aminobutyric acid	ABU	Lysine	LYS
Arginine	ARG	Methionine	MET
Aromatic unknown	ARO	Ornithine	ORN
Asparagine	ASN	Phenylalanine	PHE
Aspartic acid	ASP	Proline	PRO
ASP/ASN ambiguous	ASX	Pyrollidone carboxylic acid	PCA
Basic unknown	BAS	Sarcosine	SAR
Betaine	BET	Serine	SER
Cysteine	CYS	Taurine	TAU
Cystine	CYS	Terminator	TER
Formyl	FOR	Threonine	THR
Glutamic acid	GLU	Thyroxine	THY
Glutamine	GLN	Tryptophan	TRP
GLU/GLN ambiguous	GLX	Tyrosine	TYR
Glycine	GLY	Unknown	UNK
Heterogen	HET	Valine	VAL
Histidine	HIS	Water	HOH

ATOM IDENTIFIERS FOR AMINO ACIDS

The atom names used follow the IUPAC-IUB rules (ref. 3) except that the Greek letter remoteness codes are transliterated as follows:

alpha - A       beta - B       gamma - G       delta - D
epsilon - E     zeta - Z       eta - H

Atoms for which some ambiguity exists in the crystallographic results are designated A. This will usually apply only to the terminal atoms of asparagine and glutamine and to the ring atoms of histidine.

The extra oxygen of the carboxyl terminal amino acid is designated OXT.

Four characters are reserved for the atom names as follows:

1-2   Chemical symbol - right justified
3     Remoteness indicator (alphabetic)
4     Branch designator (numeric)

This does not have to be adhered to strictly because the chemical symbol (element name) is defined in columns 77-78. This definition will be taken in preference.

REFERENCES

1. F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer, Jr., M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi and M. Tasumi, J. Mol. Biol., 112 , 535-42 (1977).
2. J. Biol. Chem., 241 , 527, 2491 (1966).
3. IUPAC-IUB Commission on Biological Nomenclature. "Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains. Tentative Rules (1969)", J. Biol. Chem., 245 , 6489 (1970).