Actually I was not aware of the fact that we have to deposit the structure which is most probable
biological assembly (since in PDB there are seperate representations for the asymmetric unit and
biological unit).
Also Since I dint have any experimental evidences other than PISA predictions and comparison
with the structures from different organisms, I continues to refine the model PHASER predicted.
In addition the PHASER refined model has 3 Cadmium ions inbetween the monomers strongly
coordinated by both the monomers. Hence I did not have any doubts upon this assembly. Finally
I submitted this assembly itself. and by mistake I mentioned most probably biological assembly
section while submitting the PDB, Which gave rise to all confusions.
Thanking you
With Regards
M. Kavyashree
-----Eleanor Dodson <c...@ysbl.york.ac.uk> wrote: -----
To: Kayashree M <ka...@ssl.serc.iisc.in>
From: Eleanor Dodson <c...@ysbl.york.ac.uk>
Date: 10/20/2011 03:23PM
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Biological assembly
I am sure someone has suggested this - you can submit your coordinates
to the PISA server which will give you a detailed analysis of contacts,
then you choose which grouping you think makes the most reasonable
assemblyn and take the asymmetric unit from that .
I actually like to do that while still refining - it makes coot a lot
easier to use if you are working with a compact molecule!
Eleanor
t On 10/20/2011 05:25 AM, Kayashree M wrote:
> Respected Sir,
>
> The space group is H3. if I generate the symmetry,
> it appears to be a dimer of trimers stacked one above
> the other with a rotation of 60 deg wrt each other, like
> this - A1, A2, A3 (in one trimer) stacked upon
> B1, B2, B3 (second trimer). So structure that is in the ASU
> is with A1-B1 while PISA predicts A1-B2.
>
> Thank you
> With Reagrds
> Kavya
>
> -----CCP4 bulletin board<CCP4BB@JISCMAIL.AC.UK> wrote: -----
>
> To: CCP4BB@JISCMAIL.AC.UK
> From: James Stroud
> Sent by: CCP4 bulletin board
> Date: 10/19/2011 10:41PM
> Subject: Re: [ccp4bb] Biological assembly
>
> On Oct 19, 2011, at 4:36 AM, Kayashree M wrote:
>> We have a structure which is a homodimer in the asymmetric unit.
>> PISA predicts most probable assembly as a dimer but this
>> dimeric assembly is different from what is solved (offcourse
>> we can generate the symmetry equivalent molecule and get that).
>
> This last sentence is a bit vague. Can you take the just dimer that PISA
> predicts, fit this dimer to the lattice (i.e. each monomer sitting correctly
> in density but retaining the dimeric relationship predicted by PISA), and
> then generate the complete lattice using just this fitted dimer and
> crystallographic symmetries?
>
> If so, that means that the PISA dimer is equivalent to the ASU you can
> deposit the PISA dimer as the ASU.
>
> James
>
>
>
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