Dear Kavya, If I understand your question correctly, it is about the choice of asymmetric unit for your deposition. In case of dimeric asymmetric unit (ASU), there are, indeed, a few valid possibilities and you arrive to just one of them in the course of structure solution. What you decide to deposit, is your own choice, and I would think that the PDB can suggest an alternative but they would not really insist on it (hopefully).
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. I do not want to imply here that PISA will always make a correct prediction, therefore, one should always be critical and use as much experimental evidence as possible. However, deposition of biological assembly as ASU, where possible, is always preferential irrespectively of whether the assembly agrees with PISA predictions or not. Preferential does not mean mandatory though :) I hope this helps, Eugene. On 19 Oct 2011, at 11:36, Kayashree M wrote: Dear users, 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). My question is - is it necessary that we deposit a structure, which PISA predicted as most probable assembly in PDB as an asymmetric unit & biological assembly or can we deposit a dimer (asymmetric unit) and give explanation for the biological assembly according to what PISA predicted. Other than such predictions what other criteria needs to be considered to say that one specific assembly is a biological assembly? Another question- In this case one of the chain has 3 MSE residues, while the other chain has only 2 MSE (When we change MET to MSE, there will be a huge negetive density coming up). Are there any such instances in PDB, where two homodimer (or any mer) will have different percentage of MSE? Thanking you With Regards kavya -- This message has been scanned for viruses and dangerous content by MailScanner<http://www.mailscanner.info/>, and is believed to be clean.
