Re: [ccp4bb] oxidised cys

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

Previous message:
Subject: Asso/Full Professor position in Medicinal Chemistry at University of Minnesota
From: Doug Ohlendorf ohlen {- at -} UMN {- dot -} EDU
Date: 2007-04-13

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Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-13

Subject: Re: oxidised cys
From: Mark Brooks mark {- dot -} x {- dot -} brooks {- at -} GMAIL {- dot -} COM
Date: 2007-04-13

It worked well for me, on the selenium edge. Back-soaking out the remaining
cacodylate was necessary to find the sites.

Choe's group have used this fruitfully:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=pubmed&term=greenwald+butler+choe&tool=fuzzy&ot=Greenwald+Bultler+Choe

Meignan et al propose a reaction mechanism, involving an As(+3)-thiolate
intermediate ((CH3) 2AsSR), which then reacts with free cysteines by thiol
exchange:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&term=9735293&doptcmdl=Citation

Mark

On 13/04/07, Martyn Symmons wrote:
>
> 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" < flip@KEYDP.COM>
> > 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
> > >
> > > _________________________________________________________________
> > > Express yourself instantly with MSN Messenger! Download today it's
> FREE!
> > > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> > >
> >
> >
>
>

--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE
UMR8619 - Bât 430 - Université de Paris-Sud
91405 ORSAY CEDEX

CCP4bb navigation

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

Previous message:
Subject: Asso/Full Professor position in Medicinal Chemistry at University of Minnesota
From: Doug Ohlendorf ohlen {- at -} UMN {- dot -} EDU
Date: 2007-04-13

Next message:
Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-13