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

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CCP4bb <-- 2008 <-- April 2008 <-- 04 April 2008
Previous message:
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 		Next message:
Subject: Re: DM - NCS averaging after phaser molecular replacement run-confused about coefficients
From: "Randy J {- dot -} Read" rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2008-04-04


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
>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.

I've written CD where I should say CG in the above.

Peter

________________________________

From: CCP4 bulletin board on behalf of Peter Brick
Sent: Fri 04/04/2008 18:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Error in configuration of hydroxyproline in HYP.cif



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: Error in configuration of hydroxyproline in HYP.cif
From: Peter Brick p {- dot -} brick {- at -} IMPERIAL {- dot -} AC {- dot -} UK
Date: 2008-04-04 		Next message:
Subject: Re: DM - NCS averaging after phaser molecular replacement run-confused about coefficients
From: "Randy J {- dot -} Read" rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2008-04-04


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