Dear All,
We are pleased to provide the final programme for the BSG Winter
Meeting.
***Student bursaries are now available***
To be eligible, student participants are asked to submit an abstract
(max 200 words) for a poster presentation and provide a letter of
recommendation from their
Yes - I think there is a button on the GUI to click?
Eleanor
On 11/24/2010 01:58 AM, Huiying Li wrote:
Another question on RMSD:
I have two structures of the same protein superposed with the LSQ
Superpose in Coot by matching the first ~100 residues of the N-terminal
domain. Now I'd like to
Are you sure the sequence is right? It looks like tyrosine
Phil
On 24 Nov 2010, at 12:10, Vinson LIANG wrote:
Dear all,
I'm refining a structure and find some strange triangle density on the oxygen
of Ser and Thr at the C terminus. One picture of the strange density is
attached here.
look like tyrosines to me!
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.researcherid.com/rid/B-3678-2009
On 24 Nov 2010, at 13:10, Vinson LIANG
Hi Vinson
Beyond the possibility for another type of residue as already suggested by Phil
and Mark, there is also the possibility of O-linked glycosylation of the serine
and threonine, if your protein undergoes such post-translational modification
and it has been expressed via an expression
Dear Savas and all,
Thank you very much for all your quick suggestions.
I have tried Tyr and it turns out to fit the density very well. I will have the
protein sequenced again to see if it is wrong sequece or O-linked
glycosylation.
I'll let you know if it turns out to be O-linked
Hi Vinson,
along these lines: did you check the molecular weight of your protein with
MS? This should help to answer if the molecular weight deviates from the
expected one.
Best wishes,
Linda
Savvas Savvides schrieb:
Hi Vinson
Beyond the possibility for another type of residue as already
Hi Vinson
is O-glycosylation possible at all given the origin of the protein and the
expression system used?
best
Savvas
On 24 Nov 2010, at 14:42, Vinson LIANG wrote:
Dear Savas and all,
Thank you very much for all your quick suggestions.
I have tried Tyr and it turns out to fit
Phosphoserine ?
शेखर चिं मांडे
हैदराबाद
On Wed, Nov 24, 2010 at 5:40 PM, Vinson LIANG
lwg_conrad_1...@yahoo.com.cnwrote:
Dear all,
I'm refining a structure and find some strange triangle density on the
oxygen of Ser and Thr at the C terminus. One picture of the strange density
is attached
This density does not look at all like O-glycosylation.
Best regards,
Herman
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Savvas Savvides
Sent: Wednesday, November 24, 2010 2:48 PM
To: CCP4BB@JISCMAIL.AC.UK
I think there may be two effects going on here:
I think the ears on the round spots which also feature on the more rod
shaped spots if you look closely could be related to a misalignment of
the beamline optics.
I think the change in spot shape from round to rod shaped is due to the
Hi,
The ears extended to other images but not all of them, some images do not
show any signs like this. Thanks for replying, Liz.
Best,
Hubing
On Wed, Nov 24, 2010 at 10:26 PM, elizabeth.d...@diamond.ac.uk wrote:
I think there may be two effects going on here:
I think the “ears” on the
Hi Savvas,
You're right. It shouldn't be O-glycosylation, since the protein is from
Archaea
and expressed in E. coli. Most possiblly, I think it's something wrong with the
sequence.
Thanks for your help,
Best,
Vinson
发件人： Savvas Savvides
Hi Linda and all,
Thank you very much for your suggestion.
I just help to solve the structure of this protein. And I'm not sure if the
protein is properly sequenced first. I'll confirm the sequence first. I'll let
you know if it is not the sequence's problem.
I very appreciate help from
It seems that the Fourier cat is up to no good again..
BR
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Hubing
Lou
Sent: Wednesday, November 24, 2010 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unusual diffraction spots
Dear CCP4BBer,
I recently
Hi!
I am trying to calculate shape complementarity using SC in CCP4 for nucleic
acids.
SC stopped with an error no radius found for atoms of nucleic acid residues.
I can edit in the radii for those atoms in sc_radii.lib, but am wondering what
would the recommended radii be, especially for
Can anyone please recommend a UK protein sequencing service. Our protein is
dimeric with reported molecuar weight of about 85kDa.Our funds are somewhat
limited.
Thanks in advance.
Rex Palmer
Birkbeck College, London
RexPalmer2010.homestead.com
Hey Rex,
Jeff Keen at Leeds has sequenced some of our proteins with good results.
http://www.fbs.leeds.ac.uk/proteomics
Andreas
On 24/09/2010 4:46, Rex Palmer wrote:
Can anyone please recommend a UK protein sequencing service. Our protein
is dimeric with reported molecuar weight of about
To All,
Seeking used single crystal diffraction components - Detectors, Cryo-genic
systems, X-rays sources.
We are setting up several diffraction labs and are currently seeking system
components.
Any availability - donation, for sale , salvage.
Thanks.
Peace,
Archie
Dear colleagues,
I would like to express my thanks for all of your responses. I was able to
find some reasonable initial space group hits, and now I have to fight
against divergent refinement of cell parameters, and other things, but I
hope I can solve this difficulties in some time.
Actually, I
Our group has an opening for a highly motivated postdoctoral fellow, to study
the structure of mammalian ZP domain-containing proteins that mediate egg-sperm
interaction at the beginning of fertilization. Parallel projects on different
ZP domain proteins are also available. For further
Thanks for your reply, Eleanor.
The problem I had with LSQKAB is that it ONLY outputs the RMSD for the
residue range the superpose calculation based upon. What I wanted is to
superpose the two structures with the N-terminal 100 residues, but
calculate the RMSD for the entire structure (400
Dear All,
Could you please provide me some suggestions on following.
1. Could there be difference in interaction between two proteins when produced
a) both in bacteria,
b) both IVTT (in vitro transcription and translation), and
c) one in bacteria and other by IVTT.
Could you please direct me
It is somehow related to your second question. These folks describe a method
for crystallization of low affinity complexes. I hope that helps.
Ignatev, A. et al. (2007) A size filtration approach to purify low affinity
complexes for crystallization J. Str. Biol. 159(1), 154-157
Cheers,
Mario
Producing the proteins in cell free system or bacterial expression can affect
the removal of the start methionine. Although the same rules of a small amino
acids next to the start methionine apply, different methionine aminopeptidases
tolerate certain small ones better. Depending on the which
On Wed, 2010-11-24 at 09:54 -0800, Huiying Li wrote:
I have two structures of the same protein superposed with the LSQ
Superpose in Coot by matching the first ~100 residues of the
N-terminal
domain. Now I'd like to calculate the pair-wise RMSD for the entire
pre-superposed structures
To further clarify things, the data was collected at a synchrotron beamline
with collimator size ~130*40(um*square), beam divergence ~0.3*0.1mRad. The
detector type was MarCCD.
The crystal was multiple-faced trigonal (space group P3121) the size was
about 0.1*0.1*0.15mm. The exposure time was 2s
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