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Hi Scott, That would be great if you have some references handy? Thanks very much, Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of Molecular and Cellular Biology School of Biological Sciences The University of Adelaide On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz <[log in to unmask]> wrote: > Hi Andrew, > > Based on the atoms and distances you are mentioning, these don't sound > like steric clashes, but like a chalcogen bond between the S and O atoms, > and CH...O hydrogen bonds between the O and CH3. These are common and > well-accepted interactions, but unfortunately aren't usually treated as > such by refinement programs. Let me know if you want references for these > interaction types. > > Scott > > On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall < > [log in to unmask]> wrote: > >> 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 <[log in to unmask]> >> 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 < >>> [log in to unmask]> 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 >>> >> >> > > > -- > 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 >