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Re: [ccp4bb] oxidised cys
 

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CCP4bb <-- 2007 <-- April 2007 <-- 13 April 2007
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From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-13 		Next message:
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From: Doug Ohlendorf ohlen {- at -} UMN {- dot -} EDU
Date: 2007-04-13


Subject: Re: oxidised cys
From: Martyn Symmons martainn {- at -} OSHIOMAINS {- dot -} FREESERVE {- dot -} CO {- dot -} UK
Date: 2007-04-13
Dear John
I think this is a thiol-specific reaction - where it has happened to Cys residues the Met residues appear normal. I wondered if anyone had ever used this on purpose as a heavy atom derivative. Arsenic has quite a good anomalous signal too I think.
All the best
Martyn

Martyn Symmons
Department of Pathology
University of Cambridge



========================================
Message Received: Apr 13 2007, 01:37 PM
From: "John Walker"
To: martainn@oshiomains.freeserve.co.uk
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] oxidised cys

Can methionine be modified with these two reagents in a similar manner?

Cheers,

John

--
John R. Walker, Ph.D.
Structural Genomics Consortium
University of Toronto
Toronto, Ontario
Canada

On 4/13/07, Martyn Symmons wrote:
> 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 Å).
>
> 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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>
>
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