On Monday 08 March 2010 14:11:00 Jim Fairman wrote:
> I have a similar situation so I am also curious for the answer. Refmac will
> always try to form a disulfide bond with both conformers for me as well.
From the current PDB reference document
<http://www.wwpdb.org/documentation/format32/sect6.html>
Known Problems
If SG of cysteine is disordered then there are possible alternate linkages.
wwPDB practice is to put together all possible SSBOND records. This is
problematic because the alternate location identifier is not specified in
the SSBOND record.
So it is broken by design.
Perhaps there is a work-around for refmac by adding hand-constucted
external distance constraints?
<http://www.ccp4.ac.uk/html/refmac5/keywords/keywords_5_5.html#External>
Ethan
>
> On Mon, Mar 8, 2010 at 4:55 PM, Critton, David <[log in to unmask]>wrote:
>
> > Dear CCP4BB,
> >
> > I am building a protein structure containing a pair of cysteines linked via
> > disulfide bond. This disulfide bond (i.e. the cysteine S-gamma atoms)
> > refines well at 2/3 occupancy, however the electron density suggests that
> > these cysteines each adopt a second, unlinked conformation (presumably at
> > 1/3 occupancy). I have no trouble building the alternate conformers;
> > however, refinement causes both conformers to disulfide-bond.
> >
> > I would like to know if there is a way (and how) to specify individual
> > conformers (or individual atoms) in the SSBOND record of a PDB.
> >
> > Thank you in advance,
> > David A. Critton
> > Graduate Student, Page Laboratory
> > Department of Molecular Biology, Cell Biology & Biochemistry
> > Brown University
> > Providence, RI
> >
>
>
>
> --
> Jim Fairman, Ph D.
> Post-Doctoral Fellow
> National Institutes of Health - NIDDK
> Cell: 1-865-748-8672
> Lab: 1-301-594-9229
> E-mail: [log in to unmask] [log in to unmask]
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
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