Re: [ccp4bb]: ligands in a 2-fold axis

[Daan Virtual <vdava@davapc1.bioch.dundee.ac.uk>]

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Hi

Isn't there another possibility, i.e. that the ligand binds with 50%
occupancy in the two possible orientations around a crystallographic
two-fold? Thus, looking at each monomer, the ligand interacts with the
protein in two different orientations with very similar contacts with
exactly 50% occupancy each. In order to refine this one would have to
switch off the interactions between the two
"alternate conformations" of the ligand - that is possible in CNS. As
long as there isn't any ligand atom lying exactly on the two-fold this
should work fine.

We have had a case like this with an inositol-phosphate ligand
(which has pseudo symmetry (depending on the number of
phosphates attached)) interacting with a PH domain in two different
orientations.

cheers

Daan


On Tue, 3 Dec 2002, Eleanor J. Dodson wrote:

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>
> Rongsheng Jin wrote:
> >
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> >
> > Hi there,
> >
> > My protein crystallized in the P21212 space group. It forms a homo-dimer
> > around the crystallographic 2-fold axis. There is one small molecule
> > ligand binds to each protomer. The interesting thing is that the 2-fold
> > axis goes through the middle of the ligand molecules, although the
> > ligand itself is not perfectly 2-fold symmetric. It ends up with two
> > ligands overlap with each other while the 2-fold axis goes in the middle.
> > Does anybody know how to do the refinement (CNS?) without reducing to the
> > p21 space group?
> >
> > Thanks,
> >
> > Rongsheng
>
>
>  First - if this is happened your spacegroup is not P21212 - it is P21
> with an NCS axis relating the two protein molecules..
>
>  You must first process the data with P2/m symmetry -
> once you have merged h k l and -h -k l you have lost the information
> about the ligand orientation. (lets hope you collected enough redundant
> data to cover the larger asym unit!!)
>
>  Then impose NCS restraints on the protein and look for the ligand in
> the diff map..
>
> Eleanor
>
> --
> ------------------------------------------------------------------
> Eleanor J.Dodson, York Structural Biology Laboratory,
>                   Chemistry Department,
>                   University of York, Y01 5DD Heslington, U.K.
> Tel: Work: +44 (1904) 32 82 53  Home +44 (1904) 42 44 49
> ------------------------------------------------------------------
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava@davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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