Hi, What you must deposit is what is present in the asymmetric unit of the crystal. The HEADER cards (and the publication) can describe the most likely biological assembly. Why is that: there is no reason why the crystal should conform to the biological function (and associated quaternary structure), there are examples of having the asymmetric unit different than the biological assembly. Such as a crystal asymmetric unit containing half a viral capsid.
So the PDB files contain "what you see" in the crystal, and there are places for the interpretation, such as these pictures appearing on the web page for the structure showing the most likely biological unit. Or if you (as a user) request the PDB to provide you with the coordinates for that most probable biological assembly. Fred. > Message du 19/10/11 12:36 > De : "Kayashree M" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] Biological assembly > > 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, and is > believed to be clean. >
