You should check if this residue is a part
of a glycosylation pattern (either via crude computational sequence analysis,
or if you’re lucky – by digest and peptide MS).
The density *looks like* a disordered sugar but at 2.6A this is a very
tough call.
Artem
From: CCP4 bulletin
board [mailto:
Sent: Monday, January 07, 2008
10:20 PM
To:
Subject: [ccp4bb] how to model
this density?
Dear All:
I am refining a structure at 2.6 A reslution. The protein is expressed in CHO
cell, so it might be glycosylated.
While refining an Asn residue as shown in the figure of the attachment, I found
some strange density extended beyond the side chain of Asn. The sigma level for
the fofc map of the figure in the attachment is as high as 3.0. My protein
buffer is Tris and NaCl, and the reservior is PEG and NH4Cl. I believe this is
not water mlecules. Considering the residue is Asn, I guess it might be
carbohydrate.
Is this density like a carbohydrate molecule? How to model this density?
Thanks and Happy New Year.
--
Jiamu Du
State Key Laboratory of Molecular Biology
Chinese