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 errors are not actually updated by the authors. Would it not be
>helpful if there were a mechanism to make and track useful improvements in
>deposited structures? - Perhaps suggested by members of the community to the
>authors.
>
>
>These changes could be considered as 'corrigenda' and could be documented and
>tracked - complete with an explanation of the reasoning behind the change and
>attributing the motivation and origin of the improvement.
>
>
>This would be a good way for the wider scientific community (who maybe do not
>read this bulletin board) to access the best current model without the authors
>suffering the full process of retracting and redepositing their PDB entry. The
>test for obsoleting would then be the same as for a paper - that the change
>invalidates a fundamental interpretation of the data.
>
>
>All the best
> Martyn
>
>
>
>________________________________
> From: Pavel Afonine mailto:pafon...@gmail.com
>To: CCP4BB@JISCMAIL.AC.UK
>Sent: Sunday, 20 October 2013, 19:49
>Subject: Re: [ccp4bb] Problematic PDBs
>
>
>
>Hello,
>
>
>just for the sake of completeness: this paper lists a bunch of known
>pathologies (I would not be surprised if they've been remediated by now):
>
>
>http://www.phenix-online.org/papers/he5476_reprint.pdf
>
>
>
>Pavel
>
>
>
>On Thu, Oct 17, 2013 at 6:51 AM, Lucas <lucasbleic...@gmail.com> wrote:
>
>Dear all,
>>
>>
I've been lecturing in a structural bioinformatics course where graduate
students (always consisting of people without crystallography background to
that point) are expected to understand the basics on how x-ray structures are
obtained, so that they know what they are using in their bioinformatics
projects. Practices include letting them manually build a segment from an
excellent map and also using Coot to check problems in not so good structures.
>>
>>
I wonder if there's a list of problematic structures somewhere that I could use
for that practice? Apart from a few ones I'm aware of because of (bad)
publicity, what I usually do is an advanced search on PDB for entries with poor
resolution and bound ligands, then checking then manually, hopefully finding
some examples of creative map interpretation. But it would be nice to have
specific examples for each thing that can go wrong in a PDB construction.
>>
>>
Best regards,
>>Lucas
>>
>
>
>
