Dear Bostjan, >> In case when ASU has the same multiplicity (number of chains) as the >> probable biological assembly, the latter is an ASU as well. In such a >> case, the PDB suggests to choose ASU in the form of that assembly, purely >> for simplicity. It seems to me that this is not an unreasonable >> suggestion and it would be nice if that were a common practice. > > Maybe I am misunderstanding what you are saying Eugene, but the ASU > interface may not necessarily be the biological interface.
Not at all. But if anticipated biological assembly has the same size as ASU, then one should be able to choose ASU such that it is biological assembly. Consider that, when there is more than 1 chain in ASU, its configuration may be chosen in many different ways (but not completely arbitrarily, of course). E.g., in case of heterodimeric ASU, _any_ hetero-pair of molecules in crystal is a valid ASU (even if they do not make a contact :)). By this I mean that, by applying all crystal symmetry operations and unit cell translations, one can reconstruct the whole crystal from an arbitrary hetero-pair. In case of homodimers it is slightly more complex, e.g. one has to exclude monomers in parallel orientations. > I think it is > perfectly possible that two subunits in a biological dimer, for example, > may be related by crystallographic axis, but the NCS may be a different > non-physiological crystal contact, therefore the ASU won't be the same as > the biological dimer. So I am not sure if the above applies in general. I would think (am I wrong here?) that NCS-reduced PDB entries do not represent crystal's ASU (simply because they are reduced by _non-crystallographic_ symmetry operations). In order to get the ASU, one needs to apply NCS to the content of the entry. E.g., PDB entry 1stm has 5 chains, but they do not make an ASU: applying all space group symmetry operations would not reconstruct the crystal. NCS-expansion, however, gives a 60-chain viral capsid, which is the ASU. For fun, you may state that "your" ASU in this case is 2 complementing parts of neighbouring capsids, and this would be "crystallographically correct". It is a matter of common sense (and sense of beauty perhaps) that we choose to deposit a complete viral capsid as an ASU here. Eugene. > > Bostjan > > Bostjan Kobe > NHMRC Research Fellow > Professor of Structural Biology > School of Chemistry and Molecular Biosciences > > and Institute for Molecular Bioscience (Division of Chemistry and > Structural Biology) and Centre for Infectious Disease Research > > > Cooper Road > University of Queensland > Brisbane, Queensland 4072 > Australia > Phone: +61 7 3365 2132 > Fax: +61 7 3365 4699 > E-mail: b.k...@uq.edu.au > URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe > Office: Building 76 Room 329 > Notice: If you receive this e-mail by mistake, please notify me, and do > not make any use of its contents. I do not waive any privilege, > confidentiality or copyright associated with it. Unless stated otherwise, > this e-mail represents only the views of the Sender and not the views of > The University of Queensland. > > > > > > > >> >
