[phenixbb] on determination whether a protein is a monomer or complex by phenix

[Valerie Pye]

Hi Smith,

I'm fairly sure you can not tell the oligomeric state of your protein from
an mtz and your sequence.
What you can do is calculate the Matthews co-efficient with your given unit
cell parameters and size of monomer to see how many copies of your monomer
you may have in the a.s.u.
The difficulty lies in the fact that if say you have 4 copies of your
protein in the a.s.u - this doesn't necessarily mean you have a tetramer -
they could be 4 monomers related by n.c.s - or 2 dimers....
Is it possible to solve your structure? Then you confirm your space group
and number of molecules in the a.s.u. - then look at the area of contact
between monomers to see if they are likely to be because of multimerisation
or crystal packing.

Totally agree with Tim that a better way (which you'd probably want to do
to back-up a multimeric crystal structure) is by SEC or native PAGE. You
could also try SAXS, SEC-MALS, EM, or DLS depending on the size of protein
you're looking at. You'd also want to know that you have a clean oligomer
and not an aggregate ;)

Good luck,

val

On 6 July 2015 at 12:21, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear  Tim,
>
> I mean based on the mtz file, can I know whether I will get a PDB file of
> a monomer or dimer, or trimer, or tetramer or oligomer?
>
> Best regards.
>
> Smith
>
>
>
>
>
> At 2015-07-06 18:14:03, "Tim Gruene" <tg at shelx.uni-ac.gwdg.de> wrote:
> >Dear Smith,
> >
> >I would say that size exclusion chromatography or native PAGE are better
> >experimental techniques than crystallography for this type of question.
> >
> >Best regards,
> >Tim
> >
> >On 07/06/2015 11:20 AM, Smith Liu wrote:
> >> Dear All,
> >>
> >>
> >> Suppose I have got a mtz file, and I know the aa sequence of the protein from which I got the crystal and the corresponding mtz file, will you please tell me which phenix function (program) can tell me whether my protein crystal was formed by protein monomer or by protein complex, and if formed by protein complex, how many subunits existing in the complex?
> >>
> >>
> >> Best regards.
> >>
> >>
> >> Smith
> >>
> >>
> >>
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> >
> >--
> >--
> >Dr Tim Gruene
> >Institut fuer anorganische Chemie
> >Tammannstr. 4
> >D-37077 Goettingen
> >phone: +49 (0)551 39 22149
> >
> >GPG Key ID = A46BEE1A
> >
> >
>
>
>
>
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