Re: [ccp4bb] how to model this density?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: how to model this density?
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-01-07

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Subject: Re: How to refine large moleculars?
From: Lari Lehtio lari {- dot -} lehtio {- at -} KI {- dot -} SE
Date: 2008-01-08

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

Dear Jeff:
The sequence here is NYT. I think it is glycosylated here, isn't it?
Thanks a lot.

On Jan 8, 2008 11:37 AM, Jeff Lee wrote:

> Hi,
> Do you know what is the protein sequence in this region. If it is
> glycosylated, it should have a distinctive motif (N-X-S/T). You might have
> the first NAG attached to the Asn if the motif is there.
>
> Jeff
>
>
> On Jan 7, 2008, at 7:19 PM, Jiamu Du wrote:
>
> 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)
>
>
>

--
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 <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: how to model this density?
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-01-07

Next message:
Subject: Re: How to refine large moleculars?
From: Lari Lehtio lari {- dot -} lehtio {- at -} KI {- dot -} SE
Date: 2008-01-08