Hi Ralf & Gloria, It is of course all a matter of definition, but it happens now and again that an asymmetric ligand is lying on top of a twofold axis. This is usually modeled by fitting the ligand in two orientations at half occupancy. In one of the proteins I am working on there is the carboxylic acid group of an Asp sitting on a 2-fold axis. I have modeled the Asp with 2 alternative conformations: in conformation A, the Asp side chain would clash with itself over the 2-fold axis, thus if one protein molecule has the Asp in conformation A, the twofold related protein molecule must have the Asp in conformation B (or some other conformation).
I do not know whether you would call this a Wyckoff position, but side chains of proteins do sit on top of crystallographic symmetry axes. Best, Herman -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, December 09, 2010 3:47 AM To: [email protected] Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Hi Gloria, My hobby is space group symmetry. My interest phenix development. > so I can't imagine a protein crystallographer would ever need to > apply the modulation function to a protein atom that happened to be > on one. That's true. Protein residues don't have internal symmetry, therefore they are not compatible with crystallographic special positions. (Wyckoff positions are enumerations of classes of special positions.) In the PDB molecules with internal symmetry are really rare, except for H2O and SO4. But these contribute so little to the total scattering that it isn't important to handle them in a special way. So Wyckoff positions remain foreign in the macromolecular context. Ralf ----- Original Message ---- > From: Gloria Borgstahl <[email protected]> > To: [email protected] > Sent: Wed, December 8, 2010 12:16:54 PM > Subject: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms > > I've gotten some interesting responses, that I will summarize for the > group later, but I thought I should clarify why I asked. > > I was worrying about this because I have been working out the steps > in how to determine the (3+1)D superspace group for a protein crystal. > The last step listed in IT vol C chapter 9.8, is to consider any > atoms that lie ON a Wyckoff position, and what restrictions this > would apply to the modulation function that is refined for each atom. > > My first reaction, was "Wyckoff positions?" I vaguely remember > those, my recollection from my experience was they were really cool, > but were usually in the solvent, so I can't imagine a protein > crystallographer would ever need to apply the modulation function to a > protein atom that happened to be on one. But to a crystallographer > working on a modulated mineral, it would happen all the time, I'll bet. > So maybe this was one more thing that just didn't really apply to > protein structures and lucky us we don't worry about this last step > (just as I never did model that solvent water that was on one, back > in the 90s). > > Then I thought, maybe I'm missing something, or there are special > cases out there (and so far I have heard of a disulfide bond on a > 2-fold connecting two homodimers). > > So I polled the collective knowledge of the great ccp4bb group. > > On Wed, Dec 8, 2010 at 10:57 AM, Gloria Borgstahl > <[email protected]> wrote: > > My fellow crystallographers, > > I wanted to take a poll. > > > > How many of you have ever had a protein atom on a Wyckoff position > > (AKA a special position). > > What kind of molecules have you found at special positions (it > > would have to contain the symmetry of the special position, right?) > > I'm thinking it is impossible to have a protein atom at a special > > position or am I exposing my ignorance yet again... > > > > my experience is that only once I found an atom in a special > > position, it was a strange solvent molecule, that blew my mind for > > a while until I learned about special positions in crystallography. > > > > Looking forward to your responses, Gloria > > > > > > ******************************************************************** > > **** > > Gloria Borgstahl > > Eppley Institute for Cancer Research and Allied Diseases > > 987696 Nebraska Medical Center > > 10732A Lied Transplant Center > > Omaha, NE 68198-7696 > > > > http://sbl.unmc.edu > > Office (402) 559-8578 > > FAX (402) 559-3739 > > > > Professor > > Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA > > Metabolism, Modulated Crystals, Crystal Perfection > > Interests: Manga, Led Zepplin, Cold Play, piano, BRAN, RAGBRAI, > > golf and lately superspace groups > > > > ******************************************************************** > > **** > > >
