Of course metal ions, So4 etc often lie on special positions - the
insulin hexamer is generated around Zn atoms on the 3-fold axis.
Eleanor
On 12/09/2010 01:29 PM, Ian Tickle wrote:
Of course it's always possible for an asymmetric molecule (or part of
a molecule, such as a side-chain) to lie on or near a symmetry axis,
provided it's rotationally disordered with occupancy 0.5 (assuming a
2-fold). In other words half the molecules are randomly distributed
over half of the asymmetric units in one orientation and the other
half are in the other a.u.s in the symmetry-related orientation, so
the copies never clash. The occupancy must be near 0.5 because if it
deviated much from that you would start to see breakdown of the
symmetry of the diffraction pattern (with higher Rmerge etc), and you
would likely conclude that the space group is actually a sub-group of
the original one without the symmetry axis. Obviously it will depend
on the quality of the data, the resolution and the scattering power of
the disorder part whether you are able in practice to detect such a
breakdown of symmetry.
The question here though is whether an atom (say the CG of the ASP) of
the rotationally disordered molecule/part-molecule in such a situation
necessarily lies _on_ a special position. It would be pure
coincidence if it did, for the simple reason that there's absolutely
no reason why it should do so. In other words, because it has
occupancy 0.5 (obviously it must have the same occupancy as the atoms
that it's covalently bonded to, assuming there's no other disorder
present), it must be disordered and so doesn't have to obey the bulk
symmetry. In fact, it would be equally 'happy' slightly displaced
from the special position. There will be no significant minimum in
the internal energy of the system for a disordered atom on a special
position, because the reason it's disordered is that there are no
strong interactions with the surrounding atoms, which would favour one
possible orientation over the other.
This is quite different from the original question posed by Gloria
where (I assume) we have a molecule on a special position where there
is no rotational disorder (it may still have occupancy disorder, i.e.
it may only be present in a fraction of the a.u.s). Here clearly the
occupancy may be> 0.5 for a 2-fold and so no clashes with the
symmetry mate(s) are permitted (assuming of course that the space
group is correct!). In this case the molecule itself must therefore
possess at least the symmetry of the special position, e.g. H2O or SO4
for a 2-fold, as Ralf says. Being ordered (or at least not as
disordered) such a molecule must have strong interactions with its
neighbours, so any shift off the special position would likely result
in an increase in internal energy.
Cheers
-- Ian
On Thu, Dec 9, 2010 at 11:26 AM,<herman.schreu...@sanofi-aventis.com> wrote:
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:ccp...@jiscmail.ac.uk] On Behalf Of
Ralf W. Grosse-Kunstleve
Sent: Thursday, December 09, 2010 3:47 AM
To: CCP4BB@JISCMAIL.AC.UK
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<gborgst...@gmail.com>
To: CCP4BB@JISCMAIL.AC.UK
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
<gborgst...@gmail.com>
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
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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
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