Dale, In case, I will keep it as alternating configuration.
Thanks. Kevin -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Dale Tronrud Sent: Friday, August 21, 2009 9:37 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Disorder vs configuration alternation Dear Jin, As a conceptional issue, I don't see the different between "disorder" and "alternating configuration". Disorder is present, at a site, when several alternative conformations have nearly equal energies resulting in some molecules adopting one conformation while others adopt others. Each of the molecules has an energetically sound conformation, but the density, being an average, is confusing and difficult to interpret. Your description does not seem to indicate any disorder. You report that each copy adopts a particular torsion angle, indicated clearly by your density. That's not disorder, it is just the observation that ncs related copies in the asymmetric unit differ from one another, and that is not unexpected. I'm not too interested in the rms differences between the other parts of the active site. Individual differences can be masked by the averaging in such a calculation. What is more interesting is if these COOH groups make different hydrogen bonds in each copy. If small changes in the acitve site change the interactions with this group, causing it to rotate, and this is important to catalysis, you have an interesting story - Several points along the reaction pathway in one crystal structure. If the COOH group makes no hydrogen bonds then the relevance of this observation to understanding the enzyme is murky. Dale Jin, Kevin wrote: > Hi everybody > > Can anyone educate me about structural/residue disorder for conceptual > clearance? > > I have characterized a protein containing multiple subunits. In the active > site of each subunit, a terminal carboxylate group on reaction intermediate > presents a different configuration with clearly electron density support. The > structural superposition of these subunits clearly shows that the residues > from each active site are invariant (rmsd 0.26 Ang), except this carboxylate > group with alternating configuration. Further structural superposition of > this model against other available structure homologs indicates the active > site is also invariant( rmsd. 0.76 ~ 1.02 Ang). The torsion anglea of the > carboxylate group vary from 16 degree, 56 degree and then to 89 degree. It > may be too good to believe it even if the electron density is very clear > here. > > In attached figure, the electron density is scaled to 1.0 sigma and the > resolution of this model is 1.6 Ang. > > Since such alternating configuration can represent the tautomerization in > chemistry, shall I consider such configuration difference as a disorder or > real configuration alternation? > > Thanks, > > Kevin > > > ---------------------------------------------------------------------- > -- >
