Hi, All
Suppose I have two proteins A and B, they are structurally homologous,
however the sequence identity is only about 20%. A has crystal structure
available, so if I want to model protein B, what's the best way to do it? I
don't think I can just thread the sequence of B to A structure because
Scientist
Protein Crystallography
Permanent, full time
The Australian Synchrotron, a major new national facility, provides researchers
from Australia, NZ and overseas with a powerful tool for scientific and
industrial research. The facility has applications in fields as diverse as
structural mo
To clarify: I am not implying that I've worked with many proteins that
express better in XL1-blue cells than they would express in BL21(DE3) or
such if cloned into a pET vector or similar. In fact I can probably recall
only one or two that expressed *better* in XL1 cells. However in the good
old da
Hello Artem,
We express almost all our proteins in BL21 derivatives. It sounds
like you've worked with many proteins that express/behave better in
XL1-Blue?
ho
UC Berkeley
-
XL1-Blue is a strain
Kewl :)
I have one online but its ability to graph has been switched off because of
the inanity of my hosting provider. The source for the script (which also
calculates m.w. and extinction/absorption theoretical values) is here
http://www.xtals.org/prop_calc_script.perl
and the data file it reads
With Word 2004 and OSX, I use bookends (OSX-only)
http://www.sonnysoftware.com/
instead of endnote. I've found bookends to be simpler to use.
Dave
--
Donnie Berkholz wrote:
On 14:02 Mon 04 May , Paul Paukstelis wrote:
Openoffice with Zotero/Firefox works very nicely for refs.
I've found the OpenOffice plugin for Zotero to be very flaky on my Linux
system. In my experience, it's crash-prone, slow, and likely to corrupt
my document and
For Linux, there is also a program called "Bibus", which works with either
MS office or open office.. it is like endnote, just a little less..
It is in the Fedora repo, possibly also Ubuntu..
On Mon, May 4, 2009 at 10:48 PM, Donnie Berkholz wrote:
> On 14:02 Mon 04 May , Paul Paukstelis wro
On 14:02 Mon 04 May , Paul Paukstelis wrote:
> Openoffice with Zotero/Firefox works very nicely for refs.
I've found the OpenOffice plugin for Zotero to be very flaky on my Linux
system. In my experience, it's crash-prone, slow, and likely to corrupt
my document and totally screw up referenc
Word of caution: The pI depends on the sum of the (unknown) local pKa,
and various calculators have varying opinion about the 'normal' pKa values.
It would be good to state which source of pKa's is used.
BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Beh
Hello all,
I had the worst time the other day finding an online tool to calculate
charge versus pH values for an input protein sequence. There are many
programs for calculating the isoelectric point (pI), put not many that
output a complete titration curve.
Because such information is often us
One thing to check is whether there is too much DNA in the
transformation reaction. This is sometimes a reason for failed
transformations, be it DNA from regular minipreps, PCR DNA or
ligation reactions etc.
Raji
On May 4, 2009, at 3:57 PM, b...@freesurf.fr wrote:
This story is rather puz
Hi all,
I am aware of programs to plot (or analyse) the difference
between the main chain angles of two monomers. I wondered there might
be such facility for side chain angles. I consider this might also be
useful to analyse, e.g., changes in conformation for different
crystals or dif
This story is rather puzzling indeed, and it is difficult to see why in
case of toxicity one would have transformation problems with that one
strain in particular.
Also, I am wondering how likely it is that a combination of toxicity and
leaky expression would lead to transformation problems in the
Ed Pozharski wrote:
On Sat, 2009-05-02 at 11:50 +0100, mb1pja wrote:
.. but OSX gives you Unix AND you can run Word /Powerpoint without
rebooting. And you get a user-friendly ergonomic windowing system that
kicks the out of XP/Vista/KDE/Gnome...
best wishes
Pete
I guess you should c
On Sat, 2009-05-02 at 11:50 +0100, mb1pja wrote:
> .. but OSX gives you Unix AND you can run Word /Powerpoint without
> rebooting. And you get a user-friendly ergonomic windowing system that
> kicks the out of XP/Vista/KDE/Gnome...
>
> best wishes
>
> Pete
I guess you should check some
Postdoctoral Position - Center for the Study of Systems Biology at the
Georgia Institute of Technology
Postdoctoral applications are sought to work with Professor Jeffrey
Skolnick in the Center for the Study of Systems Biology at the Georgia
Institute of Technology. Specific areas include t
Postdoctoral Position - Center for the Study of Systems Biology at The
Georgia Institute of Technology
Postdoctoral applications are sought in Bioinformatics to work with
Professor Jeffrey Skolnick. Available projects include the
development and application of novel algorithms to predict p
XL1-Blue is a strain of E. coli. Whether it is or isn't an expression host
depends on the definition, and I am not going to argue semantics.
The T5 promoter works with regular garden variety RNApol of E. coli.
Therefore ANY E. coli strain is an 'expression host' for vectors that
contain this promo
I am using ccp4-6.1.1 on linux and OSX .
I have a problem with uniquefy adopting the cell dimensions of the "wrong"
data set during an rfree copy.
When I use uniquefy to copy an rfree column from one data set to another. Is
it normal for uniquefy to replace the cell dimensions in the data to the
Have you tried M15[pREP4], which are the cells Qiagen would like you to
use? You can at least use pREP4 + your expression host, and have
repressor expression to prevent leaky expression. That can help you get
colonies of transformants.
Engin
On 5/4/09 7:04 AM, atul kumar wrote:
xl1-blue is
Using pQE30, any E. coli is an expression host. Because it uses the
T5 promoter, you don't need an E. coli strain carrying the T7 RNA
polymerase (so, you don't need a "DE3" strain).
As noted by Artem, you are most likely having a leaky expression
problem. However, it is odd that DH5a will
Hi Atul,
T5 could be leaky, and Qiagen used to distribute expression strains with
extra lac repressor provided from the additional pREP4 plasmid. Those
strains are M15 and SG13009. In combination with double operator site on
pQE-30, this is usually enough to control potential toxic effects of
xl1-blue is not an expression host,since i have cloned it successfully,i need
to transform into expression host, i am able to transform it into dh5 alfa,but
not in any of expression host
From: ar...@xtals.org [mailto:ar...@xtals.org]
Sent: Mon 5/4/2009 6:32 PM
T
Hi,
You are using a pQE vector which has a T5 promoter. T5 is a native-like
promoter, recognized by the E. coli RNA polymerase - and this means that
even with lac operatorsupstream there is a huge amount of leakage in this
system. If your protein is even moderately toxic then you have issues.
You
i have cloned my gene successfully into qiagen vector into pqe30 but i do
transformation of this into BL21,pLys,Rosseta,C41, i dont get any colonies,comp
cells are good other clones give good no of colonies upon transformation.
can someone help???
thanks
atul
-Original Message-
From: CC
Dear Lidefeng,
One "Tassos" afterthought; you are sure you traced the chain correctly? It is
not that both change make a crystal contact and then each go their own
(disordered) way?
Best regards,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Beh
*PhD Programme in Structural Biology in Vienna*
The Medical University of Vienna (MUW), the University of Vienna
(UNIVIE), the Research Institute of Molecular Pathology (IMP) and the
Institute for Molecular Biotechnology (IMBA) announce the opening of an
*International PhD Program in* ”*Struc
Dear Li Defeng,
>From the original Email, I had the impression that the peptide was not part of
>the protein (e.g.activation peptide, substrate). If it is part of your protein
>you have a problem. If a peptide superimposes with its symmetry-mate (like you
>have), the maximum occupancy is 0.5 wh
29 matches
Mail list logo
