[phenixbb] sequence independent model building possible?

Kaushik Hatti hskaushik at gmail.com
Thu Feb 4 22:01:45 PST 2016


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.
MRN Murthy lab,
IISc, India

Stupidity is everyone’s birthright.  However, only the learned exercise it!
--Kaushik (28Oct2014)
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