Dear All,
i have solved a structure of 3.2 A. That is a PLP depended enzyme.
In their resting state, PLP-dependent enzymes are usually joined by a
covalent aldimine linkage to an essential lysine residue with a C=N bond.
This generates the so-called internal aldimine moiety.
Could anybody tell me
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Hi
I just encountered the same problem as described in the message below. I tried
to search but couldn’t find an answer, but was a solution for this problem
found?
Thanks
Marjolein
On 04 Aug 2014, at 03:59, Eze Chivi
ezech...@outlook.com.armailto:ezech...@outlook.com.ar wrote:
Hello, I
Try refining your model both ways (with and without covalent link) and see if
electron density maps give you an indication. At this resolution there will be
some model bias, so be critical.
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: rohit kumar
Dear Colleagues,
we are pleased to announce the CCP4 structure solution school at the Photon
Factory, Tsukuba. All details can be found at
http://www.ccp4.ac.uk/schools/Japan-2014
Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 4 to 8, 2014
Site:
Hi Marjolein,
I'm glad to hear that. You may also be interested in the new CCP4 online
service which hosts, among other applications, a MrBUMP service. One of
the main advantages it has is that it uses HHPred to search for MR
search models which can produce better models than the simple Fasta
All, slightly off-topic, but this might be interesting (BBC Radio 4
tomorrow @ 14:15 BST):
http://www.bbc.co.uk/programmes/b04dmxwj
For some background info see also:
http://www.theguardian.com/science/political-science/2014/aug/13/margaret-thatchers-surprising-relationship-with-dorothy-hodgkin
Aren't the many chromatographies out there sufficient? Or ultrafiltration? Can
you be a bit more specific about your needs?
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Reza
Khayat
Sent: Tuesday, August 19, 2014 9:55 AM
To:
Hi,
Does anyone have a protocol for getting rid of PEG3350 from a protein sample?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
What odds to you give us?
...I bet on disordered DTT covalently bound to the protein.
Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 19 Aug
Remie,
Actually, concentrating of a protein solution is not the best approach to
removing low MW impurities, gel filtration chromatography is more reliable and
... faster.
Regards,
Alex
On Aug 19, 2014, at 7:03 AM, Remie Fawaz-Touma wrote:
Hi Reza, I had to do this before.
This protocol
Hi,
I guessed glycerol by looking at the figs and not reading your text. Having
read your text afterwards, you do have glycerol in the solution. My guess is
glycerol.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160
Reza,
If your protein is not too small (20 kDa), use a spin-column (i.e., desalting
column) with G-25 sephedex. It is CHEAP, fast, and the recovery is good. We
have even used them to adjust buffer concentrations or to remove micellar
detergents; we have used protein concentrations up to 10
Hi Bernhard,
It is difficult guess with two dimensional images. Is it possible a metal
coordinated by Cys-Sulfur and one or two acetate ions?
HTH,
Partha
Sent from my iPhone
On Aug 19, 2014, at 10:12 AM, Bernhard Loll l...@chemie.fu-berlin.de wrote:
Dear all,
We are currently working
Hi,I used COOT mask map by atom selection and cut out a fragment of the map, then exported it and now I tried to open it in QTMG.It displays it as a unit cell, I want one for a presentation, how can I combine it to display one image ?Thank you,Patrick
Free 3D Earth Screensaver
Watch the
You can create the same selection in CCP4mg, display the map and then,
clicking on the first icon on the left underneath the map's name, use Clip
and choose your atom selection. Then, in Clip Radius you can adjust how
much of the map you want to see.
Hope this helps,
Jon
On 19 August 2014
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Hi Alex,
I disagree with you even though GF is always the last step in my purifications.
Because it involves concentration before and after the GF so during the
concentration you can already be doing the buffer exchange.
You use GF when you want to purify other protein impurities if they are
Hi Rohit,
Mass spectrometry might give you the most definitive answer, if you can
denature or digest and identify the adduct.
In addition, PLP has a characteristic absorbance that can change based on
its chemistry, and so you may be able to probe it spectrophotometrically,
although this might
There was indeed a bug for which I apologise. It is fixed in version 0.3.11
which will be filtering through CCP4 updates in due course. In the mean time if
you get this bug you will have to revert to an earlier version (0.3.6 or
earlier I think), or you can get it (Linux version) from
Hi,
i am concentrating my protein using centricon filter, but it is
precipitated soon. Please help me solving this problem.
Thanks.
Prashant Deshmukh
Dept. of Biophysics,
NIMHANS,
Bangalore 560 029,
E-mail:prashantbiophys...@gmail.com
Mob.No.: +919620986525
Hi Prashant,
You need to go really slow when concentrating, not more than 2000 rpm for
proteins that precipitate easily. Your protein could be sticking to the sides
of your centricon or precipitating. Follow the manual in getting your protein
out of the filter (I believe you invert the filter
Hi Prashant,
I typically stop the centrifuge once in awhile and pipet up/down to prevent
the sample from over-concentrating. Depending on how sensitive the sample
is, you may want to do this once every 10-60 min.
Hope this helps,
Chris
On Tue, Aug 19, 2014 at 1:42 PM, Prashant Deshmukh
Contract
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Job Category Sanofi/Genzyme - Scientific, Framingham, MA
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A highly
motivated candidate is
Prishant,
Remember that concentrating by almost any method is a non-uniform process. In
your case, right at the membrane the concentration is much higher than in the
surrounding solution. As Chris says, frequent efforts to keep the solution
well mixed can prevent precipitation. As you mix,
The planarity and symmetry rules out a mixed disulfide with DTT. Wrong
size/shape for glycerol. Without looking at your crystallization reagents,
I would have suggested something like an S-hydroxycysteine adduct of
something like 2,4-pentanedione or a dehydrated MPD alkene. Could
pentanedione be a
Some things to try to increase solubility:
1. Move the buffer pH away from the expected pI. Proteins have minimum
solubility near their pI values.
2. Add solubilizing agents to the solution, e.g., 20-50% glycerol. (This
may alter you crystallization screening strategy)
3. Include some inert salt
Dear Prashant,
I have been working with a protein-protein complex expressed in mammalian
cells, and that complex in very poorly soluble. Even with 500mM NaCl in the
buffer, I cannot concentrate the complex to above 3 mg/mL. I tried an old
school technique and precipitated my protein complex
Be aware that some buffers are temperature sensitive and change pH, if this
pH change heads toward the pI of the protein it can crash out.
On Tue, Aug 19, 2014 at 6:37 PM, Prince, D Bryan
dbryan.pri...@astrazeneca.com wrote:
Dear Prashant,
I have been working with a protein-protein
Dear All
i would like your advise about a good software for x-ray powder diffraction. i
used to work on a software provided from phillips but i am not anymore.
i will mainly need it for refinement for my compounds
Thanks very much
Nancy
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