Non-symmetric tetramers: you can check out Tete-Favier et al (1993),
Acta Cryst. D49, 246: the quaternary structure was assumed to have local
222 symmetry. It turned out this was not exactly the case: the actual
symmetry of the object (the molecule) was pseudo 2t2t2t. So in
addition to 2-fold
Hi Fred,
If your tetramer show negative cooperativity between the 4
sites for ligand binding, then it is possible to get a tetramer with
(say) only one subunit occupied by ligand, which can introduce
considerable asymmetry if ligand binding gives rise to a hinge type
closure of
Thurs., July 29th 2010
EBI
Morning,
I think Andrew meant PDB 2gd1 and 1gd1 (has 4 NAD)
DOI10.1016/0022-2836(88)90130-1
Miri
On Wed, 28 Jul 2010, A Leslie wrote:
Hi Fred,
If your tetramer show negative cooperativity between the 4 sites for
ligand binding, then it is possible to
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] non-symmetric tetramer ?
Non-symmetric tetramers: you can check out Tete-Favier et al (1993),
Acta Cryst. D49, 246: the quaternary structure was assumed to have local
222 symmetry. It turned out this was not exactly the case: the actual
symmetry of the object
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
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
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
Fred,
Two cents - I think the P1 SAXS solution should strongly guide your choice
of symmetry constraint above all else in this case: do any of the
symmetry-restrained shape reconstructions *improve* the statistics (chi) and
stability of the shape (NSD) when compared to the P1 result? Also, it
: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
To: CCP4BB@JISCMAIL.AC.UK
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
So, that was my previous question.
Em 29-07-2010 14:14, Phoebe Rice escreveu:
You don't have to keep the same number of symmetrical
contacts.
Original message
Date: Thu, 29 Jul 2010 14:13:56 -0300
From: Fredccp4bb.l...@gmail.com
Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd
No, constraints do not improved the Chis, but also don't harm them much.
Which NSDs, from selection or superposition (damsel or damsup)? The
superposition ones:
P1
egp1p_04-1.pdb !! Reference file
egp1p_12-1r.pdb !! NSD = 0.912
egp1p_05-1r.pdb
Dear CCP4bb,
Could someone please, point me to some references about non-symmetric
tetramers? If I have a tetramer composed by 4 identical subunits, it'll
always have a P4 point group symmetry?
Thank in advance,
Tomb
I had a tetramer with 222 symmetry--1f38 and related entries. Is that what
you mean?
Jacob
- Original Message -
From: Fred ccp4bb.l...@gmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, July 28, 2010 1:31 PM
Subject: [ccp4bb] non-symmetric tetramer ?
Dear CCP4bb,
Could someone
The symmetry of a homotetramer will depend (in
part) on how many types of interfaces it has. Some sort of 2-fold
symmetry is probably more likely. Crystallization unit cell is another
matter, and depends on contact interfaces. We study a protein that is a
homotetramer that has two different
Dear Tomb,
if your tetramer (oligomer in general) is part of the asymmetric unit the
crystal's space group can be independent from the tetramer.
Tim
On Wed, Jul 28, 2010 at 03:31:45PM -0300, Fred wrote:
Dear CCP4bb,
Could someone please, point me to some references about non-symmetric
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