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[ccp4bb] Error in configuration of hydroxyproline in HYP.cif
 

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CCP4bb <-- 2008 <-- April 2008 <-- 04 April 2008
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From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
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Subject: Re: Error in configuration of hydroxyproline in HYP.cif
From: "Brick, Peter" p {- dot -} brick {- at -} IMPERIAL {- dot -} AC {- dot -} UK
Date: 2008-04-04


Subject: Error in configuration of hydroxyproline in HYP.cif
From: Peter Brick p {- dot -} brick {- at -} IMPERIAL {- dot -} AC {- dot -} UK
Date: 2008-04-04
Dear All,

My colleague Erhard Hohenester has noticed that there is an error in the cif
definition file for hydroxyproline distributed with CCP4 version 6.02 and
used by Refmac, Coot (and Phenix).

In collagen a hydroxyl group is bonded to the CD atom of the prolyl ring to
give an R configuration.
[IUPAC: (2S,4R)-4-hydroxypyrrolidine-2-carboxylic acid]

The monomer dictionary file HYP.cif incorrectly specifies the S
configuration about the CD atom.

In HYP.cif the chirality is specified by the sign of the chiral volume
formed by a scalar triple product:

HYP chir_01 CA N CB C negativ
HYP chir_02 CG CB OD CD positiv

The second line should be:
HYP chir_02 CG CB OD CD negativ

Alternatively, one could change the atom order.

Peter

--
Peter Brick,
Division of Cell and Molecular Biology,
Blackett Laboratory, Imperial College,
Prince Consort Road, London SW7 2BW, UK
Tel: 020-7594-7704 Fax: 020-7589-0191

CCP4bb navigation

CCP4bb <-- 2008 <-- April 2008 <-- 04 April 2008
Previous message:
Subject: Re: Off topic: Real funny until someone loses a Happy Meal
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-04-04 		Next message:
Subject: Re: Error in configuration of hydroxyproline in HYP.cif
From: "Brick, Peter" p {- dot -} brick {- at -} IMPERIAL {- dot -} AC {- dot -} UK
Date: 2008-04-04


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