[phenixbb] Restraints file for a new amino acid residue

Joseph Noel noel at salk.edu
Fri Aug 13 11:26:31 PDT 2010

Thanks all for the advice. Basically that is what I have been doing. It is actually an oxidized cysteine to sulfenic acid. I am refining the site as alternative conformers with the normal Cys, the single oxidation state to sulfenic acid (CSO) and the double to sulfinic acid (CSD). I know that CSO is in the phenix library but it adds hydrogens to the amino group every time I run elbow or ready set. I then I have to edit the PDB file to delete the hydrogen or Phenix will not refine. I also have problems in COOT. It will not let me move the residues torsional angles. I have checked other structures in the PDB and the density fits perfectly with the structures of many such oxidized systems but for some reason Phenix is giving me some problems. I was going to create a "new" residue and explicitly define the oxygen as charged rather then protonated since the pKa of sulfenic acid is quite low. Maybe the problems all stem from refining this particular position with three alternative "conformers", each conformer of which is chemically distinct. For now, I have CSO labeled as convention BCSO for conformer B. Cys is ACYS.

Joseph P. Noel, Ph.D.
Investigator, Howard Hughes Medical Institute
Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
The Salk Institute for Biological Studies
10010 North Torrey Pines Road
La Jolla, CA  92037 USA

Phone: (858) 453-4100 extension 1442
Cell: (858) 349-4700
Fax: (858) 597-0855
E-mail: noel at salk.edu

Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
Web Site (HHMI): http://hhmi.org/research/investigators/noel.html

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