I would submit the coordinates to PISA to analyse the buried surface area for each momnomer and see if there are differences. It is pretty common that some copies have much lower B values and therefore are better defined..
Eleanor On 29 November 2017 at 17:15, Denis Rousseau <denis.rouss...@einstein.yu.edu > wrote: > I want to thank everyone on the BB for their comments about the > differences in the homodimeric protein. I had done a superposition of the > structures and found no differences that could account for the differences > in the water occupancy I observed. However, I had not compared the B > factors which was suggested by Mike Garavito. When I did, I saw the same > thing he mentioned; namely in one subunit the Bs were in the mid to low 40s > but in the other they were in the mid to high 50s and the metal in question > went from 42 to 56. I assume these differences originate from crystal > packing effects as suggested by several. > > Best > > Denis Rousseau > > > > ________________________________________ > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Gloria > Borgstahl [gborgst...@gmail.com] > Sent: Wednesday, November 29, 2017 10:32 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] AW: Differences in a homodimer protein > > I have seen this in MnSOD. We had a tetramer in the ASU and each > active site had different ligands in our peroxide soak. I assumed the > crystal lattice can influence these things or it is inappropriate > metal incorporation. I would highly recommend doing ICP-MS on a > dissolved crystal and on your purified metalloprotein to make sure > your metal incorporation is 100% the metal you want. > > On Wed, Nov 29, 2017 at 1:58 AM, <herman.schreu...@sanofi.com> wrote: > > 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 > > > > ________________________________ > > > > >
