> What always perplexed me is how does this system arise, meaning the precision of the ratio between dimers and monomers in solution necessary to reproducibly crystallize a 2x2 + 1 assembly.
Well, if there is an equilibrium between monomers and dimers (and it could be a very slow equilibrium), then whichever species gets depleted as crystallization proceeds would be replenished by the equilibrium?
On 06/07/2016 01:25 PM, Artem Evdokimov wrote:
> Sometimes the dimer isn't all there :)
>
> My favorite example is http://www.rcsb.org/pdb/explore/explore.do?structureId=5FFI
>
> which is a structure that our group at Monsanto solved about five years ago, but being in Industry we got scooped by Academia -- this happens all the time, but I digress :)
>
> In that structure there are two dimers, plus one monomer (total of five monomers per ASU). The monomer has a different conformation, which is why it's not a part of any dimer (including the symmetry mates). What always perplexed me is how does this system arise, meaning the precision of the ratio between dimers and monomers in solution necessary to reproducibly crystallize a 2x2 + 1 assembly. What I mean by reproducibly is that the two structures (determined independently, one by us and one by the authors of the 5FFI entry) are virtually identical and are both of the 2x2+1 variety, even though the expression and purification methods were not the same, nor are the crystal conditions... so it's not a fluke.
>
> Artem
>
> - Cosmic Cats approve of this message
>
> www.harkerbio.com <http://www.harkerbio.com>
> 'From quantum states prohibited by laws of physics to those prohibited by the township ordinance'
> (loosely adapted from Stanislaw Lem)
>
>
> On Tue, Jun 7, 2016 at 12:22 PM, Sudhaker D <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Dear sir/madam,
> Recently i have submitted a PDB at RCSB (PDB deposit). the protein is crystallised in C121phase group and there are six asymmetric molecules are present in Unit cell, I have got few comments from wwPDB annotation, one of which is given below in the name of Biological assembly
>
> Biological Assembly
> You reported that the biological assembly of this structure is dimeric.
> But we could not make the complete three dimer using all chains.
> We presumed that chain B and D make the dimer, chain e and F make the dimer.
> But chain A and C did not make the correct dimer.
> If the biological assembly should be dimeric,
> would you please provide the information of three dimers ?
> e.g. B+D = dimer1, E+F=dimer2, A+ moving C with symmetry operation -x,y,1-z= dimer3, et c.
>
>
> So please kindly give me suggestions, how to find out symmetry operations and -x,y,1-z for dimer three
>
> Regards
> sudhaker
> --
> Sudhaker Dharavath
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067.
> +919013926882 <tel:%2B919013926882>.
>
> http://www.jnu.ac.in/Faculty/gourinath/Lab_Members.htm
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
|