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Re: [ccp4bb] how to model this density?
 

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CCP4bb <-- 2008 <-- January 2008 <-- 07 January 2008
Previous message:
Subject: how to model this density?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-07 		Next message:
Subject: Re: how to model this density?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-07


Subject: Re: how to model this density?
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-01-07
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jiamu
Du
Sent: Monday, January 07, 2008 10:20 PM
To: CCP4BB@JISCMAIL.AC.UK
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)


CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 07 January 2008
Previous message:
Subject: how to model this density?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-07 		Next message:
Subject: Re: how to model this density?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-07


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