I second Phoebe's suggestion. Looks like another molecule to me. If you are
doing molecular replacement you may need to get creative about trimming. When
we had a case like that it wasn't until the third person worked on it that we
go a solution because he trimmed the model differently than the
I completely agree with Quyen. One of the many definitions of freeze is to
make extremely cold. It is grammatically correct to say freezing your
crystals, especially since, as you point out, everyone reading it knows
exactly what you did, and which definition of freeze you were referring too.
Sometimes you can distinguish disorder from the other possibilities if you have
enough structures with the same protein. We have several examples where part of
the ligand is not visible in the maps, but there is clear distortion of the
ligand binding pocket to accommodate the missing piece. for
My intent with the troll joke was to give a humorous reminder that a little
self promotion is ok, but a couple times a day is annoying. Orcus means troll,
as in Internet troll, meaning one who subverts the intended use of the site and
is annoying people. You have made a number of on topic posts
James makes an important point. I've come to regret my joke as showing poor
manners. I hesitate to add to more email that no one cares about, but I do
think it is important to contribute the idea that the positive tone of this
forum needs to be protected. I apologize, and suggest my comments
My favorite part of the german humor link:
Some German humorists such as
Loriothttp://en.wikipedia.org/wiki/Vicco_von_B%C3%BClow use seriousness as
means of humor.
On Apr 2, 2012, at 1:38 PM, Bosch, Juergen wrote:
Hm, last I checked my passport said German - still think I can make lots of
What is the single Latin word for troll?
Kendall
On Apr 1, 2012, at 3:06 PM, Kevin Jin
kevin...@gmail.commailto:kevin...@gmail.com wrote:
“I hope and believe that this is not the case. Even basically-trained
crystallographers should be able to calculate andinterpret difference maps
of
I suspect that sometimes the protein chaperones the tag, which is solvent
exposed some fraction of the time. Try very slow loading or batch binding.
Kendall Nettles
On Mar 26, 2012, at 8:15 AM, Petros Giastas
peg...@pasteur.grmailto:peg...@pasteur.gr wrote:
Dear all,
I am expressing
proteins.
Best regards,
Kendall Nettles
On Apr 19, 2011, at 3:48 PM, Savvas Savvides wrote:
Dear colleagues
We are working on a large bacterial protein (featuring a large number of
repeats) that appears to copurify with a lot of other proteins after
Ni-affinity chromatography and gel-filtration
the protein with
iodoacetic acid to generate uniform modification of the cysteines, but then we
realized we could get then same homogeneity with 20-50mM BME.
Kendall Nettles
On Apr 15, 2011, at 4:09 PM, Michael Thompson mi...@chem.ucla.edu wrote:
Hi All,
I was wondering if anyone knew
You might also try to control the degree of oxidation using the microwave, and
setting up trials after different numbers of cycles of heating.
Kendall
On Apr 12, 2011, at 12:41 PM, Jim Pflugrath wrote:
Frances Jurnak published a paper in 1986 on PEG impurities and purification.
As I
of half the protein. We assume this is the misfolded protein. We pellet this
and have dozens of structures using the supernatant. So maybe your aggregation
is a feature and not a bug.
Kendall Nettles
On Mar 29, 2011, at 8:10 PM, Neeraj Kapoor wrote:
Hi All,
I am trying to express a kinase
Very interesting discussion. I wonder if the inexperienced user of PDB really
exists? I don't know anyone off-hand who would really make use of information
from hydrogen positions but not understand the issues. Although I hear they
have been sighted in the Everglades
a major science center in
Palm Beach County, Florida, focusing on biomedical research, technology
development and drug design.
A post-doctoral fellowship position is available to study nuclear receptor
signaling and structure based drug design in the laboratory of Associate
Professor Kendall
a major science center in
Palm Beach County, Florida, focusing on biomedical research, technology
development and drug design.
A post-doctoral fellowship position is available to study nuclear receptor
signaling and structure based drug design in the laboratory of Associate
Professor Kendall
If using Coot, you can also merge molecules on the original and all symmetry
related pdb files that you saved, which will automatically renumber the chains
for you.
Kendall Nettles
Are you talking about the respective ligand with progesterone or estrogen
receptor ligand binding domains? That has been done many times. Larger
pieces of the receptor have proven more difficult.
Adding 10uM compound in the fermentation media is the traditional route,
because a significant
Hi Mariah,
We have had one case of this, with two partially overlapping conformations
of a ligand, which is not yet published.
Model in both ligand conformations. Then edit the PDB to give them the same
Chain ID, but with alternative conformations for each atom, or each one that
is different.
,
but the physiological dimer is apparent in the crystal packing.
Kendall Nettles
On 12/11/08 11:09 AM, Santarsiero, Bernard D. [EMAIL PROTECTED] wrote:
In parallel with the discussion around this off-CCP4-topic, are they any
good examples of the opposite case, where the protein is a monomer
, Kendall Nettles wrote:
CCPMG is launching X11 right before it quits. Could it relate to the
version
of X11? Coot was not working with the version that updates with the
OSX, so
I had to install the Xquartz version to get Coot to work.
Kendall
On 7/25/08 10:53 AM, Jendrek [EMAIL
I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix
version, and QtMG 1.99.0. In each case, the program does not start. I did
get a problem report for pyton, shown below.
Mac ppc dual 2.7 GHz, OSX 10.5.4
X11= XQuartz 2.3.0(xorg-server 1.4.2-apple5)
Any suggestions would
the same problem and discovered that in order to start CCP4MG the
X11
must be closed.
So, just quit your X11 and then start again. It worked fine for me.
Andrzej
Kendall Nettles wrote:
I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix
version, and QtMG 1.99.0
Hi,
Thanks to everyone for suggestions on making disulfides. I do have another
question.
Can anyone suggest some references for structures showing that a small
molecule ligand binds differently in closely related proteins?
Thanks,
Kendall
--
Kendall W. Nettles, PhD
Assistant Professor
I'm trying to engineer a disulfide bond into a protein that has several
other cysteines.
My question is whether there is a crystallization friendly reducing agent
that can be used to prevent oxidation of the free cysteines without breaking
the disulfide?
Also, can I expect 100% disulfide
Phoebe,
We were able to purify the estrogen receptor DNA binding domain with a
6his-tag. After cutting off the tag and re-applying to the Ni-NTA matrix,
the protein did not stick to the beads. We had some low resolution crystals
that contained a second protein and DNA, which suggests to me that
We have been quite happy with our crystallization robot from Innovadyne. It
transfers from deep well blocks to crystallization plates, and very reliably
sets up 200nl + 200nl drops. We have tried smaller drops with decent
success, which works better with certain plates. It can be easily
Simon,
We routinely obtain structures from protein solutions with a big pellet of
ligand in the bottom of the tube. For co-crystallizations we add 1mM
compound to a 0.3mM solution of the protein and incubate overnight. Many of
the compounds are only soluble to 50micromolar, so we get a lot of
.
A post-doctoral fellowship position is available to study nuclear receptor
signaling and structure based drug design in the laboratory of Assistant
Professor Kendall Nettles.
Candidates should have a PhD degree and experience in protein
crystallography and/or a good background in molecular biology
We have found that our His-MBP fusion doesn¹t bind well after we cut off the
protein of interest, and are trying to remove it. We have to use very low
salt, cold temp, and slow loading rates. You might also try batch instead of
column loading. We have also had good luck adding 1-2M urea to uncut
I am looking for information on short courses on data collection,
processing, and refinement.
Thanks,
Kendall
--
Kendall W. Nettles, PhD
Assistant Professor
Department of Cancer Biology
The Scripps Research Institute
5353 Parkside Dr.
Jupiter Fl 33458
office 561-799-8851
fax 561-799-8805
cell
I installed Coot 0.3.3-3 from the Binary:
Reading Package Lists...
Building Dependency Tree...
The following extra packages will be installed:
coot-shlibs
The following NEW packages will be installed:
coot
1 packages upgraded, 1 newly installed, 0 to remove and 67 not upgraded.
Need to get
I have a question about how to show certain h-bonds with CCP4MG. I¹d like to
show a specific bond between an Arg and Glu, but not other H-bonds made by
the Arg. How can I do this?
Thanks!
Kendall
I¹d like help in interpreting some mystery density in a structure.
I¹m writing a paper about soaking the apo-estrogen receptor with different
ligands. The apo structure is already released, as pdb code 2B23. The
question is whether there is a mystery molecule in the pocket of the apo
receptor. If
Sabine,
There are protocols to modify surface residues that can help with
crystallization, and make the protein less soluble. Unfortunately, I¹m
drawing a blank on the details. I remember someone in Andrzej Joachimiak¹s
group was working on this as a rescue approach for the structural genomics
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