Re: [ccp4bb] oxidised cys

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

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From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-04-13

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From: Ethayathulla Abdulsamath ethaya_aiims {- at -} REDIFFMAIL {- dot -} COM
Date: 2007-04-13

Subject: Re: oxidised cys
From: Martyn Symmons martainn {- at -} OSHIOMAINS {- dot -} FREESERVE {- dot -} CO {- dot -} UK
Date: 2007-04-13

A possible modification for cysteine that adds extra density is S-(dimethylarsenic) cysteine (CAS). Requires DTT and cacodylate buffer conditions however. And does not crosslink so far as I know.

Has been seen in a number of structures from cacodylate conditions - eg. one of the Xrcc4 structures

cheers
Martyn

Martyn Symmons
Department of Pathology
University of Cambridge

========================================
Message Received: Apr 12 2007, 06:06 PM
From: "Flip Hoedemaeker"
To: CCP4BB@JISCMAIL.AC.UK
Cc:
Subject: Re: [ccp4bb] oxidised cys

I've actually seen something like this on disulfides (or at least I think
so, I havent seen your density obviously), turned out it was model bias in
MR, if I used a different template for MR the feature went away. This was
high resolution stuff (~1.0 Ã…).

Flip

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
artem@xtals.org
Sent: Tuesday, April 10, 2007 20:44
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] oxidised cys

Hi Stefano,

How certain are you that this link is truly what you think it is? If I
understand what you're saying - you want to create a (thioperoxythio) link
- this chemistry should be hideously unstable. Can you explain this using
disorder, or perhaps the residual density is a symmetry artifact?

Regards,

Artem

> Dear all
> in my structure I think I can see an oxidised Cys in cys-SO. Refining
> cys-SO
> I observe a residual density between the oxigen of one oxidised cys and
> the
> one of the other molecule in AU.
> I'd like to try to refine it as cys-SO-OS-cys. I didn't find an example of
> it in the pdb database. Could anyone tell me whether there are other
> cases?
> I guess I just didn't find them.
> Second question:
> How could I "explain" to refmac that there is the OO bond?
> I tried to write a line similar to the one for SSBOND in the pdb header
> OOBOND 1 CEA A 42 CEA D 42
> but refmac couldn't care less...
>
> thanks in advance
>
> Stefano
>
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: : Crystallographic Programs on AMD computers
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-04-13

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Subject: Unusual Difference Fourier near Methionines
From: Ethayathulla Abdulsamath ethaya_aiims {- at -} REDIFFMAIL {- dot -} COM
Date: 2007-04-13