Dear Fabien,
Cases like that crop up from time to time. You shouldn't treat this peptide
in any way differently than any other peptide. If you're reasonably sure
about the peptide's sequence - BLAST it against a wide database (nr for
example). Like others pointed out, just make sure that it's not a piece of
something that's already part of your principal polypeptide. The latter is
very common (but could be easily verified).
Sequence-wise I am sure I don't have to mention that at 2.2A there is a lot
of possible ambiguity: D/N, Q/E, K/R/Q (disordered end), T/V, and so forth.
Artem
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Fabien
Bergeret
Sent: Friday, October 30, 2009 10:09 AM
To: [log in to unmask]
Subject: [ccp4bb] Supplementary density
Hello
We’re resolving a structure of a soluble protein and in the electronic
density map (maximum resolution at 2.2Å), we observe a supplementary
density that does not belong to the protein. This density is present in
two different crystalline forms obtained in different crystallization
conditions.
This density could be represented by an oligopeptide ~10 residues long
for which there is no ambiguity about its polarity. Furthermore, side
chains are quite easily visible and a sequence can therefore be assigned.
The deduced sequence doesn’t belong to the sequence of the protein of
interest, meaning that the oligopeptide has been co-purified and
co-crystallized.
Has somebody met a similar situation? Could you please give us some
advices in terms of refinement, validation, etc.?
Thanks in advance
Best regards
Fabien
PhD student
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