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:[email protected]] On Behalf Of Fabien Bergeret Sent: Friday, October 30, 2009 10:09 AM To: [email protected] Subject: [ccp4bb] Supplementary density Hello Were 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 doesnt 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 [email protected] <mailto:[email protected]>
