A vacancy for a Faculty Position (Assistant Professor) in the Department of
Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS),
Bangalore, INDIA.
Candidates who have research experience in membrane protein crystallography and
Cryo-EM are encouraged to apply.
Here
DESCRIPTION
The Roll-Mecak lab at the National Institutes of Health in Bethesda,
Maryland is seeking to hire an expert researcher in the area of structural
biology with emphasis on X-ray crystallography or electron microscopy of
large multi-subunit complexes. Candidates should have expertise in
Relevant to this discussion, the 2018 ACA meeting in Toronto will have a
session on
"Best practices for building, refining, and analyzing ligands in macromolecular
structures”
co-chaired by Anna Gardberg and Kurt Krause.
I expect this session will include case studies of structures that went
Trevor,
I can share our recent experience correcting the record about a misplaced
ligand binding site. It represents one possible way to deal with erroneous
structures.
Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited
by another group in 2006 suggested that the
Trevor,
I can share our recent experience correcting the record about a misplaced
ligand binding site. It represents one possible way to deal with erroneous
structures.
Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited
by another group in 2006 suggested that the
A postdoctoral position is available immediately to participate in an
inter-disciplinary research program on structural immunology at the Institute
of Human Virology of School of Medicine, University of Maryland, Baltimore, MD.
Candidates are expected to work on ongoing research projects in
Sorry if this is an insulting question, but did you store it in enough glycerol
to prevent it from freezing? Proteins don't like freeze/thaw cycles,
especially slow ones.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jai mohan
Hi Trevor,
I think you should also email the authors of the key paper in your field that
you mention. They should be told that the structure they used to create the
model of the mechanism was incorrectly interpreted and should have the
opportunity to write a correction to their paper.
Best
Dear all,
I realized I didn't properly aknowledge the team who made PDB REDO. So let me
please correct my mistake by citing here the PDB REDO references (as found on
the PDB REDO website) and providing a list of interesting papers to all :
- Joosten RP, Long F, Murshudov GN, Perrakis A.
Dear Jaimohan,
With high amount of purified protein (like obtained in recombinant expression)
they are likely to form higher oligomers if they have intrinsic property of
association. With time the content of oligomers do increase. In SDS-PAGE even,
you will see a faint band of oligomer. This
Hello Jaimohan,
Is it SDS-PAGE gel or Native PAGE gel ?. Theoretically SDS-PAGE is
supposed to show monomers and Native PAGE oligomers
On Tue, Jun 27, 2017 at 8:27 AM jai mohan <
0cab66323371-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear all,
> I am working on a Red Fluorescent
Are you boiling your samples? Seems funny that under SDS PAGE there should be
dimers, unless there is a disulfide link. If so, reducing agents (DTT, TCEP,
BME) should take care of this.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Smith Liu
Sent: Tuesday, June 27,
it was not stable for frozen storage. if necessary，using protein fresh without
frozen
发自网易邮箱大师
在2017年06月27日 20:22，jai mohan 写道：
Dear all,
I am working on a Red Fluorescent Protein (His-Tag) molecular weight around
27kDa. After purification I ran a SDS page, the band at 27kDa confirms the
Dear all,I am working on a Red FluorescentProtein (His-Tag) molecular weight
around 27kDa. After purification I ran a SDSpage, the band at 27kDa confirms
the monomer. The protein was stored at -20C, aweek later again I ran a gel,
this time I saw another new band between 50-60kDa, it confirmsthe
Dear colleagues,
EMBL-EBI (http://www.ebi.ac.uk/) is running a worldwide survey to understand
usage of its resources (there are several dozen, including UniProt, Ensembl,
ChEMBL, EuropePMC, PDBe, EMDB/EMPIAR and many more). We would like to ask you
to forward this request within your
I think the PDB (and Gerard DVD) got the answer with their quite new validation
report provided for each entry.On the other hand PDBredo (Tassos & Co) is an
excellent tool to compare a currently deposited structure and its reprocessed
version (although it doesn't tell about the phasing).
Dear Bernhard,
I totally agree with you and it was absolutely the meaning of my first email
while thinking the used F were coming from Adrian's data. And by the way of the
second as well. This being said what about groups that publish always poor
structures ? Ins't it in some way dishonest ?
I agree: I don’t think this is fraud, and was never even suggesting it. If it
were fraud, _I_ at least would back-transform my structure so that there
weren’t horrible red and green blobs all over the place…! I think it’s just
sloppy - and the question remains, as posed by the original
I beg to differ. You are not pulling a murthy simply by depositing a poor
or even wrong structure. Although the borderline beteeen sloppy work (and
selfdeception) and reckless misleading of others can be floating, real
cases of fraud and fabrication are almost exceptionally rare.
Best, br
On Jun
Dear Adrian,
OK, I understand. You might be perfectly right. Moreover as I wrote it is
difficult to tell something from a single mono view picture.And as you are
pointing out their Ramachadran plots doe not look good at all. So they are poor
crystallographers. But the question that remains is
On the subject of withdrawal of entries from the PDB, I just flag up another
interesting aspect.
Four years ago I was Visiting Fellow in a colleague's lab, and in the course of
the year I determined, refined and deposited 4 good structures, authored by me
and my colleagues who were part of the
What tiny fraction of the gazillions it would cost to store all the raw
data, would be enough to arrange the training courses needed to get the
ballooning population of practitioners up to speed, he mused idly.
On 27/06/2017 09:21, Goldman, Adrian wrote:
That’s quite something. To me, this
That’s quite something. To me, this thread raises another issue: I see a lot
of comments about extracting the last little bit from every byte of data
collected - but that’s not our main problem. Our main problem appears to be
shoddily-done refinement of data that are in fact perfectly decent
Hi Trevor,
Some of my colleagues came across a misinterpreted structure published in
Acta D., a couple of years ago.
They raised the issue with the editors of Acta D., who were most helpful in
getting the issue sorted out.
My impression is that the journals are the responsible for the papers
It can't hurt to try to work with the author, and it's the only way
to get the current PDB file out of the database. If you don't get the
response you want you can still go ahead and look for a venue to publish
your own interpretation.
Having a paper to go with the model is not only a
Note that in most cases a structure may only be obsoleted with the written
agreement of a senior author. From experience it's by far the best approach to
work together with the original authors on a correction, in any case. Goodwill
is an important thing.
If you wish, you can go it alone and
Hello,
I think it makes sense to have a look at the policy of the PDB concerning
obsoleting structures:
The publication is retracted. The associated PDB entry will be obsoleted if
requested by the journal. If a request has not been received, the wwPDB will do
its best to contact the depositor
I have come across a key paper in my field that describes an enzyme mechanism.
Their work is based on a deposited structure – by other authors - that is
incorrectly interpreted.
Is there a process for removing a demonstrably wrong structure (deposited by
others) from the PDB and replacing it
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