Confusion In Pdb File Format

Question

[GouthamAtla]

The PDB I was looking at 3G7W has different format. For e.g, the amino acid 207 has 2 C-Alpha atoms which are almost overlapping and the residue is not three letter code as defined in standard pdb file format .It is AASP and BASP.

> ATOM   1641  N   ASP A 207     -30.543   8.702 -37.961  1.00 19.64    
> N   ATOM   1642  CA AASP A 207     -29.455   7.750 -38.178  0.50 21.97
> C   ATOM   1643  CA BASP A 207     -29.436   7.777 -38.202  0.50 21.46
> C   ATOM   1644  C   ASP A 207     -28.400   7.750 -37.066  1.00 21.11
> C   ATOM   1645  O   ASP A 207     -27.496   6.924 -37.070  1.00 21.07
> O   ATOM   1646  CB AASP A 207     -28.809   7.946 -39.564  0.50 23.45
> C   ATOM   1647  CB BASP A 207     -28.720   8.133 -39.514  0.50 22.20
> C   ATOM   1648  CG AASP A 207     -27.925   9.192 -39.658  0.50 25.90
> C   ATOM   1649  CG BASP A 207     -29.590   7.925 -40.748  0.50 23.92
> C   ATOM   1650  OD1AASP A 207     -27.521   9.760 -38.620  0.50 28.07
> O   ATOM   1651  OD1BASP A 207     -30.321   6.915 -40.823  0.50 23.90
> O   ATOM   1652  OD2AASP A 207     -27.622   9.597 -40.803  0.50 29.33
> O   ATOM   1653  OD2BASP A 207     -29.522   8.775 -41.663  0.50 26.96
> O

I wrote a program for calculating the distanced between CA atoms, which takes the position of CA Atom and a cutoff radius, but because of this different format ( 2 CA for one amino acid ), the position of given CA is not in sync with the position in file.

Any ideas how to handle this situation ?

Answer 1

[David Westergaard]

The format is not different from other PDB files. It is just that usually column 17 is empty. In this case, it is not. This is also indicated by the occupancy column (55-60), which is <1. This means that the atom is not found in the same position in all crystals (More info). The occupancy indicates the fraction of crystals having the atoms in the specified position.

I don't think it would be unreasonable to use a mean of coordinates, each weighted by their respective occupancy.

[wdiwdi]

Nitpick: The occupancy applies to a single crystal, not a plurality. In that single crystal, the placement of some atom is variable - there are two or more possible (local minimum) positions relative to the constant part. Usually, there is more than one atom involved (a group of atoms can be flipped, for example), and these atoms do not independently fall into one of the possible locations, so when selecting a set for display, you need to check the group label (if it is set correctly), or perform more advanced auto-perception of groups.

[David Westergaard]

Nitpicks are the best, and you're absolutely right.

[Hamish]

FYI the wwPDB documentation for the PDB file format can be found at:

http://www.wwpdb.org/docs.html#format

The section on the ATOM records is:

http://www.wwpdb.org/documentation/format33/sect9.html#ATOM

Please note that the wwPDB suggest the use of the mmCIF/PDBx or PDBML formats for new development due to the limitations of the PDB format when dealing with larger structures (see http://www.wwpdb.org/news/news_2013.html#22-May-2013).