Hmm
So the backstory for the problematic ligand R12 in this thread is that a
sharp-eyed worker at the wwPDB recently spotted that there was an error
compared with the original 1999 paper. Correcting the R12 ligand is a friendly
gesture from the PDB as it appears that the error must have been the authors' -
the atom correcting the R12 ligand has been inserted by the PDB staff rather
than retreived from a deposited structure.
It is a shame the same helpful approach is not always applied. One current
example I spotted is a separate 'problematic ligand' 5AX which has been added
by the wwPDB to at least four other authors' entries, starting in 2006 with the
latest in 2009.
5AX is basically a fragment ligand which the PDB software produces if a NAG has
wandered too far from its Asn sidechain during refinement. If 5AX is generated
during the PDB processing of a deposition, then it really should be highlighted
for the authors as a geometric issue - rather than, as in these cases, being
simply added to the coordinates.
Reading the authors' papers for the 5AX-containing entries makes it clear that
they never expected anything other than NAG to appear in their deposited
coordinates.
And given its artifactual production during deposition, 5AX should never have
'escaped into the wild'.
So if a retrospective fix can be applied to R12 (which similar in lacking an
atom) then it seems to me that, in fairness, a clean up of the 5AX entries
should be arranged.
Yours (not holding his breath),
Martyn
From: Rachel Kramer Green kra...@rcsb.rutgers.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 6 November 2013, 16:49
Subject: Re: [ccp4bb] Problematic PDBs
Dear Martyn,
wwPDB staff regularly reviews and remediates PDB data and related
dictionaries such as the Chemical Component Dictionary (CCD).
As part of our on-going remediation efforts, the chemical
components in the archive are regularly reviewed to ensure the
correctness and the completeness of the chemical representation.
Such reviews show that in some cases, the author has failed to
provide a complete description of the chemistry. To address any
such errors, the definitions are corrected. The chemical name and
formula are changed in the PDB file, but the coordinates are not
changed.
In the case of entry 3CBS, issues were found with the chemical
component definition for its ligand R12. The methyl group was not
in the deposited coordinates and it was missing from the original
definition. In addition, the bond order in one of the
carbon-carbon bonds was incorrectly defined. The CCD definition
for R12 was updated in 2011 to add the methyl group and to correct
the bond order based on information in the primary citation. The
coordinates for this PDB entry were not changed. Therefore, in
accordance with wwPDB policy, the file was not obsoleted.
Sincerely,
Rachel Green
Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.rutgers.edu
Twitter: https://twitter.com/#!/buildmodels
Facebook: http://www.facebook.com/RCSBPDB
On 10/21/2013 6:28 AM, MARTYN SYMMONS wrote:
As a postscript it might be worth mentioning one problematic ligand that
suggested to me a way to correct some of the errors mentioned in this thread
R12 is indicated as 9-(4-HYDROXY-2,6-DIMETHYL-PHENYL)-3 in the most
recent Coot monomer library. But in the PDB ligand description it is
9-(4-hydroxy-2,3,6-trimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenoic acid
with an additional carbon C16. To make a long story short this ligand was
originally deposited missing this extra methyl goup in 1999 (as part of 3CBS)
and then apparently updated in 2011 by the PDB.
(the relevant lines in the cif are
snip
R12 C16 C16 C 0 1 N N N ? ? ? -6.631 1.502 0.990 C16 R12 44
R12 H1 H1 H 0 1 N N N ? ? ? -6.602 1.511 2.080 H1 R12 45
R12 H23 H23 H 0 1 N N N ? ? ? -6.422 2.503 0.613 H23 R12 46
R12 H24 H24 H 0 1 N N N ? ? ? -7.619 1.186 0.656 H24 R12 47
snip
with the ? ? ? indicating that refined coordinates were not available at the
time of the update. There was initially an explanation line at the end of the
cif:
snip
R12 Other modification 2011-10-25 RCSB CS 'add missing methyl group,
re-define bond order based on publication'
snip
But this has mutated for some reason (premature stop codon?) over the past
year to the following.
snip
R12 Other modification 2011-10-25 RCSB
snip
Obviously the full correct ligand could not have been incorporated into the
PDB entry coordinates without these undergoing a full obsolete - supersede
process (somewhat embarrassing perhaps as one author is now a wwPDB PI ;)
But it is frustrating for users of the PDB that in such cases easily
correctable
