Re: [ccp4bb]: Crystal packing

[Timm Maier <tmaier@chemie.fu-berlin.de>]

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Dear Lan Xu,

In my opinion, your different crystal forms as well as the size of buried
surface are good indicators for a dimer in solution. However, you might
need more criteria:
on the one hand, there are some more characteristics of the potential
dimer interface you might check: residue conservation in related proteins,
hydrophobicity, surface complementarity ... , but on the other hand a
physical measurement of the oligomerization state in solution might be
even more interesting: You might try classical lab methods such as
size exclusion chromatography or analytical ultracentrifugation, but most
interesting and exact is probably measuring small angle X-ray scattering
(SAXS) of your protein solution. Sample requirements are pretty close to
what you probably need for crystallisation and the determination of the
oligomerisation state should be straight forward with this method and is
less error prone then the indirect measures from sedimentation behaviour
or gel filtration ( What are the biophysical measures indicating that this
is a monomer ? - Maybe your dimer is really compact or has an unusual
shape not covered by ordinary data interpretation e.g. in light scattering
or gel filtration ??? )
How similar are the crystallisation conditions for the different crystal
forms and how close are they to the native conditions for your protein,
e.g. regarding osmolarity and pH ?

Bye 

Timm

> Hi, all. I have a question regarding crystal packing and protein contact.
> I have solved the structure of a receptor-binding protein in two 
> different space groups. Form I is P2221, Form II is C2221, both have one 
> molecule in an asymmetric unit. Recently, we used molecular replacement 
> to solve the structure for the third crystal form (Form III). It belongs 
> to C2221, but has two molecules in one asymmetric unit.
> When we examine the crystal packing of these three crystal forms, the 
> same dimer is present in all three crystal forms. However, all the 
> biochemical and biophysical evidence suggest that the protein is a 
> monomer in solution.
> A buried surface per subunit in the dimer is ~1206 Å2, which represents 
> ~5.5% of the surface area of the monomer.
> My questions are how do we distinguish between a biological dimer or a 
> dimer because of crystal packing? Whether a buried surface area of only 
> 5.5% of the total surface area is stable for a dimeric interaction? Is 
> there any reference that I can refer to?

____________________________________________________________________________

                 TIMM MAIER
                           Proteinkristallographie
                           Institut fuer Kristallographie
                           Takustr.6
                           14195 Berlin

                           tmaier@chemie.fu-berlin.de                   
____________________________________________________________________________