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[ccp4bb] how to model glycosylated residues?
 

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CCP4bb <-- 2008 <-- January 2008 <-- 08 January 2008
Previous message:
Subject: how to model glycosylated residues?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-08 		Next message:
Subject: Re: resolution & R-free
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-08


Subject: how to model glycosylated residues?
From: Max Crispin max {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-01-08
Dear Jiamu,

The density is definitely carbohydrate. The N-links are highly conserved so build N-acetylglucosamine (NAG) beta 1-Asn. Both the C2 acetyl group and the C6 group lie outside the ring so look for the diagonal bulge in your density to assign the orientation. To sanity check your torsion angles you may with to consult Petrescu et al. A statistical analysis of N- and O-glycan linkage conformations from crystallographic data. Glycobiology. 1999 Apr;9(4):343-52 and http://www.dkfz.de/spec/glycosciences.de/tools/pdbcare/.

From your picture, you may be unable to build the next beta 1-4 NAG. As you are using the CHO system, if you see additional denistity off the C6 (which I don't think you do) this is likely to be alpha 1-6 fucose.

If you are careful to position the NAG, refmac should detect the linkages.

Best of luck!
Max Crispin

================================================
Dr Max Crispin
The Division of Structural Biology
The Henry Wellcome Building for Genomic Medicine
University of Oxford
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Oxford, OX3 7BN
Lab: 01865 287551
Mob: 07889 932694

College address:
Dr Max Crispin
Lecturer in Biochemistry
Oriel College
Oxford OX1 4EW
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CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 08 January 2008
Previous message:
Subject: how to model glycosylated residues?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-08 		Next message:
Subject: Re: resolution & R-free
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-08


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