 |
 |
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:[log in to unmask]] On Behalf Of Jiamu Du Sent: Monday, January 07, 2008 10:20 PM To: [log in to unmask] 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 Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)