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

[Shinya Fushinobu <asfushi@mail.ecc.u-tokyo.ac.jp>]

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Another example is the crystal structure
of allosteric L-lactate dehydrogenase, having
a fructose 1,6-bisphosphate molecule exactly on
the 2-fold axis, in the mixed state (50% occupancy).

Iwata S, Kamata K, Yoshida S, Minowa T, Ohta T.
T and R states in the crystals of bacterial
L-lactate dehydrogenase reveal the mechanism
for allosteric control.
Nat Struct Biol. 1994 1(3):176-85.

:           Dept. of Biotechnology, Univ. of Tokyo
:                                 Fushinobu Shinya
:               http://enzyme13.bt.a.u-tokyo.ac.jp
: Flying Arrow      asfushi@mail.ecc.u-tokyo.ac.jp
 > > > > >>>>>>---------------------------------->>


On 2002.12.03, at 16:14, Daan Virtual wrote:

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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
>> ------------------------------------------------------------------
>>
>
>
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> Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
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