Re: [ccp4bb] oxidised cys

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

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 11 April 2007

Previous message:
Subject: high temperature factors
From: Michael Colaneri colanerim {- at -} GMAIL {- dot -} COM
Date: 2007-04-11

Next message:
Subject: AW: antibody refinement in REFMAC with Kabat numbering
From: Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM
Date: 2007-04-11

Subject: Re: oxidised cys
From: stefano ricagno ciciulus {- at -} HOTMAIL {- dot -} COM
Date: 2007-04-11

I agree with all you that it is "risky chemistry"
the problem is:
these 2 cys are pointing to each other but there is plenty of room for 2
more atoms between the 2 S atoms, so they are too far for a SS bond. The 2
molecules are related by ncs and not crystallographic symmetries.
The data are from a SAD dataset on Fe peak wavelength (so a lot of radiation
damage for sure)
There is very strong density between the oxygens, which I modelled in the
density.
I attach a snapshot from coot (fo-fc is at 3 sig 2fo-fc is at 1.5 sig).
I would like to try to refine as SOOS to see what refmac5 gives me.
If someone has any other idea I am very happy to listen to it.
The protein is a ferredoxin (which lost 2 Fe ions) but I thought that
placing 2 Fe3+ in place of the oxygens was even more risky...

cheers
stefano

>From: zac wood
>To: stefano ricagno
>Subject: Re: [ccp4bb] oxidised cys
>Date: Tue, 10 Apr 2007 12:01:17 -0700
>
>Hello Stefano,
>
>Is it possible that you have a mixture of disulfide and cleaved
>(radiation-damage) disulfide? I have seen this sort of thing before. Is
>this a synchrotron data set?
>
>Best regards,
>
>Zac
>
>
>On Apr 10, 2007, at 1:29 AM, stefano ricagno wrote:
>
>>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/
>
>
>------------------------------------------------------------------------
>--------------------
> Zachary Wood, Ph.D.
>
>Institute of Molecular Biology Office Phone:
>541-346-4080
>Howard Hughes Medical Institute Lab Phone: 541-346-5874
>372 Willamette Hall FAX:
>541-346-5870
>University of Oregon e-mail:
>zac@uoxray.uoregon.edu
>Eugene, OR 97403
>USA
>------------------------------------------------------------------------
>---------------------
>
>
>
>

_________________________________________________________________
Don't just search. Find. Check out the new MSN Search!
http://search.msn.click-url.com/go/onm00200636ave/direct/01/

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 11 April 2007

Previous message:
Subject: high temperature factors
From: Michael Colaneri colanerim {- at -} GMAIL {- dot -} COM
Date: 2007-04-11