[phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold!

Joseph Noel noel at salk.edu
Wed Aug 4 04:53:25 PDT 2010

Hi Ralf and Pavel,

Unfortunately, Phenix didn't recognize a disulfide bond should exist between the sulfur atoms of DTT and the side chain sulfur atom of the cysteine residue in question. I position everything well in the Fo-Fc and 2Fo-Fc maps and ensured the two sulfurs were approximately 2.1 A apart. However, after refinement the DTT molecule moved so the two sulfurs in question where nearly 3 A away. Maybe this is because it is a mixed disulfide between a DTT molecule and a side-chain Cys rather then what most programs expect which is a disulfide between two Cys residues. Is it possible I need to define the complete chemical entity as a hetatm (the disulfide linked Cys residue? Is there a way to specify that a covalent bond should exist between the SG atom of the Cys in question and the S atoms of DTT with DTT lying across the crystallographic two-fold given its internal 2-fold symmetry?

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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