[phenixbb] differentiate Glu/Gln and Asp/Asn from Electron Density?

Kaushik Hatti hskaushik at gmail.com
Wed Feb 10 22:14:25 PST 2016


In continuation to my earlier thread (subject: sequence independent model
building possible?), I have built model into density without knowledge of
sequence for a data diffracted to 1.9A resolution.  Current R/Rfree is
15/19, phaser error=16.88 degrees with no Ramachandran outliers.

Is there a way we can differentiate between Glu/Gln, Asp/Asn and sometimes
Thr/Val directly from density?  I have considered the local environment
(hydrophobic/hydrophilic/polarity pockets, possible hydrogen bonds/other
interactions, buried/exposed, etc...) in choosing one over the other
confusing pairs of amino acids.  However, I am not absolutely certain in
many places.

A BLAST of this sequence against all non-redundant protein sequence
database yield highest hit of 80% sequence identity.  Hence, we are still
not sure of sequence of the contaminant protein which got crystallised and
want to decipher sequence directly from the structure.

Thanks for any pointers/suggestions,

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