Re: [ccp4bb] oxidised cys

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 12 April 2007

Previous message:
Subject: Calculating apolar/polar surface area
From: "Ibrahim M {- dot -} Moustafa" I {- dot -} moustafa {- at -} PSU {- dot -} EDU
Date: 2007-04-12

Next message:
Subject: Additive screens
From: Brian Mark brian_mark {- at -} UMANITOBA {- dot -} CA
Date: 2007-04-12

Subject: Re: oxidised cys
From: Flip Hoedemaeker flip {- at -} KEYDP {- dot -} COM
Date: 2007-04-12

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/
>

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 12 April 2007

Previous message:
Subject: Calculating apolar/polar surface area
From: "Ibrahim M {- dot -} Moustafa" I {- dot -} moustafa {- at -} PSU {- dot -} EDU
Date: 2007-04-12

Next message:
Subject: Additive screens
From: Brian Mark brian_mark {- at -} UMANITOBA {- dot -} CA
Date: 2007-04-12