Dear Denis, I would first superimpose both monomers to see if you can find a reason why one subunit has a bound water and the other not, which would in general be flanking side chains in (slightly) different positions. Next I would look for some global differences between the subunits that could be linked to crystal contacts explaining the non-random distribution of the subunits. However, these differences might be quite subtle and difficult to detect.
As Emily suggested, you could also do some functional assay's to see if there is any positive (or negative) cooperativity between the subunits providing independent support for functional differences between the subunits. My 2 cts, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Denis Rousseau Gesendet: Dienstag, 28. November 2017 20:04 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Differences in a homodimer protein Hi BB members I have a homodimeric protein, which contains metal centers. In several different derivatives I find a water molecule on a metal center in one subunit which is absent on the other. It is always the same subunit that contains the water molecule. The resulution is ~2.4 A. Is this an artifact or a functional difference? If it is truly homodimeric I would expect differences to be random. The space group is P212121. Thanks for the advice. Denis Rousseau ________________________________
