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[ccp4bb] Refining alternate ligand/autoinhibition
 

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CCP4bb <-- 2007 <-- May 2007 <-- 08 May 2007
Previous message:
Subject: Post-doc position in Illkirch (France)
From: Ronan Keegan r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-05-08 		Next message:
Subject: difficulties to determine the space group
From: Schneider Sabine paxss2 {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2007-05-08


Subject: Refining alternate ligand/autoinhibition
From: Stefan Arold s {- dot -} arold {- at -} CBS {- dot -} CNRS {- dot -} FR
Date: 2007-05-08
Dear All,

I am having trouble refining a difficult case of alternate structures in
REFMAC. In the crystal, two states superimpose:
1) Apo-protein with its own auto-inhibitory tail fixed into the ligand
binding site
and
2) Peptide-bound protein, where the peptide has displaced the
auto-inhibitory tail.
this also includes alternate side-chains of the protein ligand binding
site, according to the apo state or peptide-bound state

I was hoping that assigning 'A' and 'B' alternate states (for 'apo' and
'peptide-bound') to the protein chain (chain A)
[ex:
ATOM 62 C ATYR A 17 20.856 42.150 21.476 0.60
75.23 C]

and state 'B' to the peptide
[ex:
ATOM 87 N BALA D 513 9.910 69.145 50.780 0.40
20.00 N]

would do the job - but unfortunately, even though refmac refines this
structure, the two states 'sense' each other, and refmac refinement
applies repulsive forces, pulling the apo-auto-inhibitory tail and the
peptide away from each other...

Neither the refmac manual, nor the ccp4bb archives helped, so I thought
one of you might...

many thanks

Stefan



--
==================================================
Stefan T. Arold, PhD
Centre de Biochimie Structurale
CNRS UMR 5048 - UM 1 - INSERM UMR 554
29 rue de Navacelles 34090
MONTPELLIER Cedex - France
email: S.Arold@cbs.cnrs.fr
Phone: +33 (0)4.67.41.77.02
Fax: +33 (0)4.67.41.79.13
==================================================

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 08 May 2007
Previous message:
Subject: Post-doc position in Illkirch (France)
From: Ronan Keegan r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-05-08 		Next message:
Subject: difficulties to determine the space group
From: Schneider Sabine paxss2 {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2007-05-08


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