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,<[log in to unmask]> 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:[log in to unmask]] On Behalf Of
>> Ralf W. Grosse-Kunstleve
>> Sent: Thursday, December 09, 2010 3:47 AM
>> To: [log in to unmask]
>> 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<[log in to unmask]>
>>> To: [log in to unmask]
>>> 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
>>> <[log in to unmask]>
>> 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
>>>>
>>>> ********************************************************************
>>>> ****
>>>>
>>>
>>
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