Re: [ccp4bb] how to model an average of two different amino acids at the same position in a crystal structure

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: programmatic symmetry mate generation
From: Robert Campbell robert {- dot -} campbell {- at -} QUEENSU {- dot -} CA
Date: 2010-04-26

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Subject: Re: how to model an average of two different amino acids at the same position in a crystal structure
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-04-26

Hi,

I you need to use altLocs to model alternative locations. A good example
is this PDB file (of course there are many more in PDB):

http://www.rcsb.org/pdb/files/1EJG.pdb

see residues #22, 25 etc. Once you have prepared a similar PDB file,
phenix.refine will take of the rest automatically.

Pavel.

On 4/25/10 3:48 PM, Seema Mittal wrote:
> Hi All,
>
> I have a structure where electron density shows that the complex
> crystallized is not in a unique conformation in the crystal lattice.
> It seems the electron density is an average of two possible
> orientations of the same complex.
>
> Since, the protein is bound to its substrate as a dimer, where the
> sequence of the two monomers (forming the dimer) is different at only
> a couple of positions, two different amino acids can be built in the
> same electron density. For example, serine vs alanine.
> From our previous experience in crystallizing the same complex, we
> know that its an averaged density. I am wondering what is the most
> accurate and acceptable way to represent it in the actual pdb file
> without complicating the analysis.
>
> I am hoping to resolve this issue by getting some inputs from this
> expert community.
>
> Thanks in advance,
>
> Best,
> Seema Mittal
>
> Graduate Research Assistant,
> Department of Biochemistry & Molecular Pharmacology,
> 970L Lazare Research Building,
> University of Massachusetts Medical School,
> 364 Plantation Street,
> Worcester, MA 01605

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: programmatic symmetry mate generation
From: Robert Campbell robert {- dot -} campbell {- at -} QUEENSU {- dot -} CA
Date: 2010-04-26

Next message:
Subject: Please remove me from this list
From: Emmanuel Prata emmanuelprata {- at -} GMAIL {- dot -} COM
Date: 2010-04-26