Dear Zhizhi,
we had a case like that. I would switch to slightly different buffer
(e.g. different pH) so crystals do not appear overnight, and then do
crystallisation screening. I bet you will have many hits in different
conditions, likely with bigger crystals.
Good luck!
Best wishes,
Tomas
On
Dear Gloria,
HHpred.
Best wishes,
Tomas
On Thu, Aug 22, 2013 at 4:14 PM, Gloria Borgstahl gborgst...@gmail.com wrote:
We have a protein sequence that probably contains OB folds. What is the
best way to search for the top structural homologs to this sequence in the
pdb? G
Dear Wei Shi,
is your ligand a small molecule? If it is a small molecule, I would
try to computationally dock the small molecule to two pockets
separately using AutoDock, and look at the estimated free energies of
binding.
Best wishes,
Tomas
On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi
is desired
but not necessary. Please see the lab website
(http://www.cshl.edu/public/SCIENCE/furukawa.html) for further
information and send CV with a brief research statement as well as 2-3
contacts for references to furuk...@cshl.edu
Best wishes,
Tomas
Dr. Tomas Malinauskas
Cold Spring Harbor
Dear Gregg et al.,
On Mon, May 12, 2014 at 4:28 PM, Gregg Crichlow gregg.crich...@gmail.comwrote:
Actually, it was noticing penG that made me mouse over it myself. After
spending many years completing a thesis on beta-lactamases, I was very
surprised - and excited - to see that on something
Dear Daniel,
here is an example of MR at 7 A:
http://www.pdb.org/pdb/explore/explore.do?structureId=4GZA
http://www.ncbi.nlm.nih.gov/pubmed/23104057
Best wishes,
Tomas
On Tue, Nov 6, 2012 at 11:06 AM, Panne Daniel pa...@embl.fr wrote:
Hi all,
I was wondering if there are examples of successful
Dear Xianchi,
unfortunately, dissociation rate constant kd 10^-6 s^-1 was just
beyond the limit of Biacore in 1999 (e.g. see Fig. 1 in
http://www.ncbi.nlm.nih.gov/pubmed/10556876). I am not sure about
these days.
As Juergen noted, you may have a problem with rebinding (you could try
to reduce
Hi Mike,
my favourite summary on B factor sharpening/blurring is here:
Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):923-32. Epub 2006
Jul 18.
Considerations for the refinement of low-resolution crystal structures.
DeLaBarre B, Brunger AT.
Hope that helps,
Tomas
On Mon, Nov 17, 2014
Hi Giulliana,
here is a nice and simple method on how to select heavy atoms for
phasing using native PAGE (please see Fig. 1):
http://www.ncbi.nlm.nih.gov/pubmed/10903954
Structure. 2000 Jul 15;8(7):R143-9.
Screening for phasing atoms in protein crystallography.
Boggon TJ, Shapiro L.
Hope that
Dear Fernandez et al.,
maybe this anti-His-tag antibody could be useful: PDB ID 1KTR, its
sequence is in the paper
https://www.ncbi.nlm.nih.gov/pubmed/?term=12054774
Hope that helps,
Tomas
On Sun, Jan 8, 2017 at 9:24 PM, Fernandez, Elias J wrote:
> Dear All,
>
> Is anyone aware
Dear Reza,
I used hydrogen peroxide (~0.1-2%?) to remove rhodamine stuck on
Superdex columns. "Pink" columns turned "white" after this kind of
treatment.
Hope that helps,
Tomas
On Fri, Jun 9, 2017 at 10:43 PM, Reza Khayat wrote:
> Hi,
>
> Sorry for the non crystallography
Dear Wenhe,
we had a similar case and extraction using CHCl3 plus CH3OH (2:1
ratio, v/v) (65 °C, 30 min) before mass spectrometry worked very well:
https://www.ncbi.nlm.nih.gov/pubmed/21743455
Hope that helps,
Tomas
On Mon, Aug 21, 2017 at 4:41 AM, WENHE ZHONG
Dear Nicola,
PDBeFold is great too: http://www.ebi.ac.uk/msd-srv/ssm/
Best wishes,
Tomas
On Thu, Feb 15, 2018 at 11:16 PM, Nicola Evans wrote:
> I have recently solved a novel structure which previously did not have any
> structural homologues (as related by sequence
Hi Pedro,
it seems PostScript files (one can easily convert to PDFs) with the
contents are here:
ftp://ftp.ccp4.ac.uk/ccp4/newsletter/nov_94/
Best wishes,
Tomas
On Wed, Jul 11, 2018 at 9:01 AM Pedro Matias wrote:
> Dear CCP4ers,
>
> Is there a PDF version of the Joint CCP4 and ESF-EACBM
he backbone peptide bond between residue i and residue i + 1.
https://doi.org/10.7554/eLife.31486.005
Best wishes,
Tomas
Dr. Tomas Malinauskas
University of Oxford
Wellcome Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
to...@strubi.ox.ac.uk
tom
solved it
(purified homogeneous crystallisation quality protein), please let us
know if possible. I thank you for your help.
Best wishes,
Tomas
Dr. Tomas Malinauskas
University of Oxford
Wellcome Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
k to the domain? Try
> periplasmic expression in E coli? The NEB pMal-p vector is my favourite for
> disulfide forming proteins, when not using mammalian cells.
>
> Zhijie
>
> > On Dec 14, 2018, at 11:57 AM, Tomas Malinauskas
> > wrote:
> >
> > Dear All,
> &
in the cell) with a known disulfide
> > pattern forms non-specific disulfide linked oligomers in the
> > extracellular media. We tried expressing it at 37 C and 30 C, and have
> > sequenced our constructs (plasmids) multiple times.
> >
> > If anyone has seen this kind of pro
Hi Sebastiano,
we often buy chemicals (including CHAPS) from Melford:
https://www.melford.co.uk/products/biochemicals/detergents-surfactants/chaps-1-g.html
It is often cheaper than Sigma-Aldrich.
Hope that helps,
Tomas
On Fri, Nov 30, 2018 at 2:42 PM Sebastiano Pasqualato
wrote:
>
>
> Dear all,
>
Dear Gerard,
you can find a copy of the page here:
https://web.archive.org/web/20110624033607/http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Scaling_experimental_intensities_with_Scala
Hope that helps,
Tomas
On Mon, Apr 15, 2019 at 4:19 PM Gerard Bricogne wrote:
>
> Dear all,
>
> In a
.
Elegheert J, Behiels E, Bishop B, Scott S, Woolley RE, Griffiths SC,
Byrne EFX, Chang VT, Stuart DI, Jones EY, Siebold C, Aricescu AR.
PMID: 30455477
Hope that helps,
Tomas
Dr. Tomas Malinauskas
University of Oxford
Wellcome Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford
Hi Kahkashan,
Indeed, homodimers formed by engineered disulfides could crystallize
readily in novel crystal forms: Banatao et al., "An approach to
crystallizing proteins by synthetic symmetrization”, 2006, PNAS, PMID
17050682.
Best wishes,
Tomas
On Mon, Mar 16, 2020 at 7:58 AM Firdous Tarique
Hi Dhiraj,
You could try a C-terminal Fc-tag if it is an extracellular protein,
e.g. see pHL-FcHis vector described in the supplement of PMID
17001101.
Best wishes,
Tomas
On Tue, Sep 22, 2020 at 6:08 PM Srivastava, Dhiraj
wrote:
>
> Hi
> I want to make my protein dimeric to increase its
Hi Hari,
I typically draw formulae using ChemDraw online, export SMILES and use
them to get PDBs/CIFs from Grade web server (Global Phasing). Both
ChemDraw and Grade web servers are free to use.
Hope that helps,
Tomas
On Sat, Jun 13, 2020 at 6:01 PM Hari shankar
Hi,
In addition to all great suggestions, I would try reductive lysine
methylation (PMID 17098187).
Good luck!
Tomas
On Thu, Jan 21, 2021 at 6:46 PM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hello, I always recommend limited chymotrypsinolysis. It's not a miracle
Hi Dhiraj,
pHLsec vector for transient and its variants for lentivirus-based
expression (PMIDs 17001101 and 30455477, respectively).
Best wishes,
Tomas
On Thu, Jun 24, 2021 at 9:42 PM Srivastava, Dhiraj
wrote:
>
> Hi all
> I am trying to express my protein in HEK293 cells for
Hi Fred,
At least Schrodinder's PyMOL 2.3.2 can open Vina's PDBQR files (with
multiple docked conformations) without any problems or additional CIFs
in my experience. Different conformations of ligands are loaded as
different states.
It if is an older version you could try to convert Vina's
Dear All,
Is it possible to add hydrogens to a specific residue using Coot?
Something like Calculate -> Scripting -> Python -> coot_reduce(0) but
targeting one residue only.
I thank you for your help.
Best wishes,
Tomas
Hi Henry,
You could try keeping selected atoms in the plane by manually editing
restraints in the CIF. Set _chem_comp_plane_atom.dist_esd to something
low. E.g.
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
Hi Kavya,
In addition to other excellent suggestions, I would recommend trying
reductive lysine methylation, which can make the protein more
hydrophobic. PMID 17098187.
Best wishes,
Tomas
On Mon, Feb 5, 2024 at 10:27 AM kavyashreem wrote:
>
> Dear All,
>
> Has anyone worked on a protein which
Dear All,
I apologize for asking a somewhat off-topic question.
I have multiple aligned PDB files loaded in PyMOL, each representing
different conformations of the same protein. I'm interested in
creating a graph displaying RMSD per residue, similar to those shown
at
the MD
simulation and had corresponding trajectories from GROMACS/OpenMM, I
transitioned away from PyMOL and used the GROMACS 'gmx rmsf' command.
Best wishes,
Tomas
On Fri, Jan 5, 2024 at 10:49 AM Tomas Malinauskas
wrote:
>
> Dear All,
>
> I apologize for asking a somewhat off-topic que
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