Clarifying... That's happened because I was talking about the symmetry
of the SAXS envelop/particle. I understand that if you consider the
symmetry of the whole particle, say a tetramer of identical subunits,
you can have the 4-fold axis when asking for 222 symmetry envelop, which
gives you a 422 envelop. I disagree with you statement "there is no
fundamental reason that a tetramer has to have any particular symmetry".
Thinking only in the low resolution envelop, that's not true. Try to
arrange 4 spheres in a non-symmetrical way keeping the same number of
reciprocal contacts.
Em 29-07-2010 13:17, Phoebe Rice escreveu:
> It sounds like you're missing something fundamental about
> 222 symmetry, but I may be misunderstanding you - there IS
> no fourfold. In fact, I think it is more common for the
> subunits within tetramers to be related to one another by
> three mutually perpendicular twofolds than a fourfold (e.g.
> the favorite classic hemoglobin has no fourfold anywhere).
> And there is no fundamental reason that a tetramer has to
> have any particular symmetry.
> Phoebe
>
>
> ---- Original message ----
>
>> Date: Thu, 29 Jul 2010 13:04:02 -0300
>> From: Fred<[log in to unmask]>
>> Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
>> To: [log in to unmask]
>>
>> Of course, 222 has not a 4 axis, otherwise it would be a 4-
>>
> fold axis.
>
>> But that's the output of the program. P4 exp. model has a 4-
>>
> fold axis
>
>> along the longest axis, while the P222 MODEL has a 4-fold
>>
> axis along the
>
>> smallest, which doesn't make any sense. Can you imagine
>>
> something build
>
>> up with 4 identical subunits and 222 symmtry, but without a
>>
> 4-fold axis
>
>> at the molecular level (I mean at the envelop resolution
>>
> level)?
>
>>
>> Em 29-07-2010 12:32, Vellieux Frederic escreveu:
>>
>>> Hi,
>>>
>>> To quote you: "even my P222 experimental envelop does
>>>
> have a 4-fold
>
>>> axis" - this is not suprising, a particle with 222
>>>
> symmetry does not
>
>>> have 4-fold symmetry. There are 3 mutually perpendicular
>>>
> 2-fold axes
>
>>> that intersect at the origin (of the "particle", of the
>>>
> molecule) [and
>
>>> for the nomenclature, these axes are named the P Q and R
>>>
> axes].
>
>>> Fred.
>>>
>>> Fred wrote:
>>>
>>>> Thanks all of you who promptly replied my question.
>>>> I should have been more precise. I was referring to the
>>>>
> symmetry of
>
>>>> the tetrameric particle (point symmetry) at the
>>>>
> molecular level not
>
>>>> at the atomic level. This question has arisen because I
>>>>
> have
>
>>>> collected some SAXS data of my protein in solution and I
>>>>
> don't have a
>
>>>> molecular model to superpose to the experimental
>>>>
> envelop. Others
>
>>>> experimental data, gel filtration and NAT-PAGE, suggest
>>>>
> a tetrameric
>
>>>> particle. On the other side, P1, P2, P222 and P4
>>>>
> experimental
>
>>>> envelops are quite different. So, I am not sure which
>>>>
> symmetry to
>
>>>> take. Considering the native state (no ligands at all),
>>>>
> 4 identical
>
>>>> subunits and that the interface of oligomarization have
>>>>
> to be
>
>>>> conserved, I would take P222 or P4. However, I can be
>>>>
> able to imagine
>
>>>> such spacial arrangement without a 4-fold axis at the
>>>>
> molecular
>
>>>> level. Indeed, even my P222 experimental envelop does
>>>>
> have a 4-fold
>
>>>> axis.
>>>> I appreciate if you could add some more comments on this.
>>>> Thanks in advance,
>>>> Fred
>>>>
>>>
>>>
> Phoebe A. Rice
> Assoc. Prof., Dept. of Biochemistry& Molecular Biology
> The University of Chicago
> phone 773 834 1723
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>
> RNA is really nifty
> DNA is over fifty
> We have put them
> both in one book
> Please do take a
> really good look
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
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