Hi all, Thank you for your suggestions. I tried the pdb file edit (making the offending atoms of both the ligand and the protein 'B' altconf), but it didn't seem to make any difference to their positions after a single round of refinement..? The atoms in the active site concern two acetyl groups - one from the substrate, acetyl-CoA, and the other from an acetylated cysteine in the protein - that I believe are poised ready for a condensation reaction. The closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3 (3.1A), but going off the density, I think these should be closer (more like 2.8 or 2.7A). It may be that I've trapped another reaction intermediate (which would be cool), but I don't think that fits the density quite as well. Any thoughts/ideas?
Thanks, Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of Molecular and Cellular Biology School of Biological Sciences The University of Adelaide On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz <horow...@umich.edu> wrote: > Hi Andrew, > > I'm curious- what are the atoms that are clashing? I worked on this sort > of thing back in my Ph.D., and so I might have some useful tidbits if, for > example, the S is clashing with a carbon of some sort. > > Thanks, > Scott > > On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall < > andrew.c.marsh...@adelaide.edu.au> wrote: > >> Hi all, >> >> I have a structure of a condensing enzyme with substrate bound. The >> active site is very tight, requiring some of the substrate atoms to clash >> with a catalytic cysteine. This means that although the substrate fits the >> density nicely upon manual real-space refinement, phenix recognises the >> clash, resulting in the displacement of substrate atoms so that they are >> outside the density. I can mostly fix this by using distance restraints, >> but I'd rather allow it to refine in a less biased manner, but ignore the >> clash. Is this a acceptable way forward? If so, is there a parameter I can >> edit to tell phenix to ignore clashes between these specific atoms? >> >> Thanks, >> >> Andrew Marshall >> PhD Candidate >> Laboratory of Protein Crystallography >> Dept. of Molecular and Cellular Biology >> School of Biological Sciences >> The University of Adelaide >> >> > > > -- > Scott Horowitz, Ph.D. > Postdoctoral Fellow > > University of Michigan > Department of Molecular, Cellular, and Developmental Biology > Bardwell lab > 830 N. University Ave, Room 4007 > Ann Arbor, MI 48109 > phone: 734-647-6683 > fax: 734-615-4226 >
