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



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On Tuesday 03 December 2002 08:49, 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..
>

Eleanor may be right, and you should definitely try processing the data in 
P21 to see if that generates an unambiguous orientation for your ligand.  But 
it is also possible to have a higher symmetry spacegroup with statistical 
disorder for the pseudo-symmetric ligand.  This is what happened for the 
complex of the Shiga-like toxin B-subunit with the "starfish" inhibitor that 
we published a couple of years ago.  The starfish molecule has pseudo-2-fold 
symmetry and it sits on a crystallographic 2-fold axis.  But the part where 
the symmetry breaks down is not involved in binding contacts or in crystal 
packing contacts.  If you have an asymmetric ligand but it doesn't induce any 
asymmetry in the protein and isn't involved in crystal packing contacts, it's 
not unexpected that it will be oriented randomly in the crystal lattice.  In 
such a case, the higher symmetry space group is just as well justified as the 
lower symmetry space group.  Higher symmetry is then a better choice because 
it involves fewer parameters.
-- 

Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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