Yes, and I just got a pdb file back from the pdb that they flagged
with over forty bad residues.
The Molprobity plot from the RCSB validation server shows zero
residues in disallowed regions. ( I got lucky, I didn't "fix" any bad
residues.)
For many of these "bad" residues, the position of the carbonyl oxygen
is very clear in the electron density. There are four copies of the
protein in the asymmetric unit, NCS was never used in structure
building or refinement, and all four copies of the residue have very
similar psi-phi values - the conformations are real and there is
nothing bad about the Ramachandran plot.
Has anyone successfully fought this "bad residue" listing? I
understand that the pdb wishes to flag problem regions, but this is
not a valid way of doing so. I can tell them where the problem
regions are in the structure if they wish.
Sue
On Sep 21, 2007, at 8:33 AM, MATSUURA Takanori wrote:
Hi,
If you checked the Ramachandran plot using PROCHECK, you may think
almost all residues belong to the most favoured, additional allowed,
or generously allowed regions of the Ramachandran plot that is the
part 1 of the PROCHECK output PostScript file.
But if you checked the part 2 of the PROCHECK output PostScript file
(Ramachandran plot by residue), you may find some unfavourable
conformations. You can get the similar results as our validation
letter.
Please be informed that since August 1, 2007 we do not use PROCHECK
values for the definition of the Ramachandran outliers.
We define the Ramachandran outliers according to the following
reference:
GJ Kleywegt and TA Jones (1996). Phi/psi-chology: Ramachandran
revisited. Structure 4, 1395 - 1400
As mentioned in the validation report.
An additional information is available in the following website:
http://xray.bmc.uu.se/gerard/supmat/ramarev.html
If you want to check your coordinate before deposition, please use our
validation server.
http://deposit.pdb.org/validate/
http://pdbdep.protein.osaka-u.ac.jp/validate/
In the validation summary letter that is in the result page of our
validation server, many of what we ask to depositors are written.
Thanks,
MATSUURA Takanori, Ph.D.
Annotators' Leader, Group of Primary Annotation,
Protein Data Bank Japan (PDBj)
Research Center for Structural and Functional Proteomics,
Institute for Protein Research, Osaka University
3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN
Tel: +81-6-6879-8634
Fax: +81-6-6879-8636
Sue Roberts
Biochemistry & Biophysics
University of Arizona
[EMAIL PROTECTED]
