Re: [ccp4bb] Double conformations of cysteine !

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CCP4bb <-- 2007 <-- July 2007 <-- 06 July 2007

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Subject: Double conformations of cysteine !
From: Prasenjit Bhaumik bhaumik {- at -} NCIFCRF {- dot -} GOV
Date: 2007-07-06

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Subject: Re: Double conformations of cysteine !
From: "Sanishvili, Ruslan" rsanishvili {- at -} ANL {- dot -} GOV
Date: 2007-07-06

Subject: Re: Double conformations of cysteine !
From: "Miller, Mitchell D {- dot -} " mmiller {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-07-06

The SSBOND record does not allow the specification of
an "alternate location indicator". The PDB practice is to
list the SSBOND record if any confirmation is in an SS-bond.
I think that refmac has problems with this since it will
try to apply the SSBOND patch to both confirmations. The
workaround is to use the LINK record in refmac for the SS-bonded
A confirmation (which allows alternate atoms to be specified) and
use a link_id of SS. Refmac should then generate the correct
restraints for the conformer involved in the disulfide bond.
Note that this should probably be listed as SSBOND in the header
for the deposited PDB file.

Regards,
Mitch

See
http://www.wwpdb.org/documentation/format23/sect6.html
http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_ssbond

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Prasenjit Bhaumik
Sent: Friday, July 06, 2007 10:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Double conformations of cysteine !

Hello,
We are trying to refine a structure using REFMAC and we are facing problem in
refining the double conformations of a cysteine residue. One conformation is
involved in formation of a disulfide linkage and other conformation is free. Is
there any way to define the restraints so that both the conformations can be
refined.

With kind regards,

Prasenjit

--
Prasenjit Bhaumik, Ph.D.
Protein Structure Section
Macromolecular Crystallography Laboratory
National Cancer Institute at Frederick
1050 Boyles Street, Building-539, Room-145
P.O. Box B, Frederick,
MD-21702, USA
Phone: 301-846-1974, Fax: 301-846-7101
E-mail: bhaumik@ncifcrf.gov

-------------------------------------------------

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CCP4bb <-- 2007 <-- July 2007 <-- 06 July 2007

Previous message:
Subject: Double conformations of cysteine !
From: Prasenjit Bhaumik bhaumik {- at -} NCIFCRF {- dot -} GOV
Date: 2007-07-06

Next message:
Subject: Re: Double conformations of cysteine !
From: "Sanishvili, Ruslan" rsanishvili {- at -} ANL {- dot -} GOV
Date: 2007-07-06