[phenixbb] sequence independent model building possible?

Edward A. Berry BerryE at upstate.edu
Fri Feb 5 11:19:42 PST 2016

Hi Kaushik,
If the polyala is somewhat complete, you can submit to DALI server and see what fold it matches.
But, with fairly complete polyala and 1.9A resolution, it should be really easy to
assign residues in a stretch of 20 or so with enough accuracy that a blast search will
identify your protein.  I did this once with 2.6 A data on a wrong protein we collected,
and the closest match was correct, even in the right species, although
homology (with my guessed sequence) was only ~50%.

On 02/05/2016 01:01 AM, Kaushik Hatti wrote:
> Hello,
> Is abinitio model building possible for a map with poly alanine model at 1.9A resolution?
> We thought we had crystallised our protein of interest X, collected data at 1.9 A and all attempts to solve protein X (which has many homologs) through MR failed.  All attempts to re-crystallise the same protein also failed.
> Now, we think the initial protein which got crystallised could be a contaminant (we don't have any crystals left from this batch to check for the sequence of the crystallised protein).  Through various methods (and a bit of luck) we have arrived at a decent map with LLG : 3600 and TFZ: 22 and R/Rfree : 37/41 (for a poly alanine model).
> I believe these scores indicate right fold.  As I still don't know the sequence information, is it possible to build sidechains directly from the map (I could only identify a couple of residues and the model largely remains PolyAla)?  Autobuild with Rebuild-in-place didn't help in identifying any more residues.
> I have also searched PDB database for similar structures. But, none of those are either from our expression system (E. coli) or organism of our protein of interest. Neither did I find any similar sequences from E. coli or our organism of interest.
> Any leads/suggestions would be helpful.
> Thanks,
> Kaushik,
> MRN Murthy lab,
> MBU,
> IISc, India
> --
> Stupidity is everyone’s birthright.  However, only the learned exercise it!
> --Kaushik (28Oct2014)
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