Dear Michael, Thank you very much for the useful comments.
Indeed, we are of course looking at it biochemically, which isn't a clear cut so far.. As you pointed out it could be a monomer in solution, but the interface between monomers within this asymmetric trimer seems too extensive (compared to those responsible for the lattice packing) not to suspect a trimer as a solution assembly. PISA suggested this asymmetric trimer as the most likely assembly but it falls into the grey region of their criteria (see attached pic.) Since it's rare, we are interested to know of other similar reports, if any, to learn how they were resolved/concluded. I believe the case you describe is not similar, as we have NO rotational symmetry (2, 3, or 4-fold) whatsoever between interacting monomers in the ASU or relating those built up by the crystallographic symmetry. Therefore I can't see how the space group information may help, but it is p212121 in case it helps boosting your morning coffee experience with symmetry pondering ... :). Cheers, Hay On Dec 11, 2014, at 3:47 PM, R. M. Garavito wrote: > Dear Hay, > > And your point is? I am not trying to be snarky (although I am just starting > my morning coffee), but to bring up the fact that CCP4BB readers need more > info to comment on your case, like space group, local interactions, and how > packed is "tightly packed." > > I have had two cases of "trimers," as my students initially called them, that > were actually a dimer and a half. The "half" dimer had its mate in another > ASU. Can it be a biological monomer that just happened to crystallize 3 > monomers to an ASU? Non-symmetric homo-oligomers are rare, but sadly cannot > be absolutely confirmed by crystallography alone, but by good old > biochemistry. The PISA website > (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) can give you estimations > of the strengths of the interfacial interactions, but they are mere > estimates. What does gel filtration say or cross linking? Does it fit with > the biology/biochemistry expected of this protein? > > Anyway, have fun with your structure, but use a lot of skepticism in your > interpretation. That will help you convince the reviewers. > > Cheers, > > Michael > > **************************************************************** > R. Michael Garavito, Ph.D. > Professor of Biochemistry & Molecular Biology > 603 Wilson Rd., Rm. 513 > Michigan State University > East Lansing, MI 48824-1319 > Office: (517) 355-9724 Lab: (517) 353-9125 > FAX: (517) 353-9334 Email: rmgarav...@gmail.com > **************************************************************** > > > > > On Dec 11, 2014, at 7:27 AM, Hay Dvir <hd...@tx.technion.ac.il> wrote: > >> Dear all, >> >> >> We have a structure of a rather tightly packed homotrimer protein in the ASU >> with no apparent crystallographic or non-crystallographic rotational >> symmetry between monomers. >> Attempting to establish the biological assembly, we are very interested to >> hear about additional similar cases you might know of. >> >> Thanks in advance, >> Hay >> >> >> --------------------------- >> Hay Dvir Ph. D. >> Head Technion Center for Structural Biology >> Technion Haifa 3200003, Israel >> Tel: +(972)-77-887-1901 >> Fax: +(972)-77-887-1935 >> E-mail hd...@technion.ac.il >> Website http://tcsb.technion.ac.il >> >
