Re: [ccp4bb] Unidentified electron density blob

[zaigham mahmood khan]

Uma, that is not something that we see regularly in the crystal structures.
But i never used PFPE either. So, you may try PFPE. If this is not PFPE,
then you may read the biology of the protein.

Also I can see green density, but these green blobs are devoid of blue
density. So i will be cautious. May be just add water molecule in each
blob, and re-run refinement. You will see a change in color of the blobs,
that may indicate something.. If red blobs appear around the water
molecules, i will consider it just a noise. Alternatively, you will see
green density connecting the water molecules...





Best wishes

-Z


Zaigham Mahmood Khan, PhD

Icahn School of Medicine at Mount Sinai
Department of Oncological Sciences
1470 Madison Avenue
New York

On Mon, Jul 2, 2018 at 10:23 PM, Uma Gabale <
0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
>
> We came across a blob of unidentified electron density in a shallow cavity of
> a bacterial protein structure (pictures attached). It is surrounded by
> residues Asp, Arg, Gln, His, Glu, Thr, and Trp.
>
> The protein was expressed in *E. coli* BL21(DE3) and purified on Ni-NTA
> followed by gel filtration. The purification buffers included Tris,
> crystallization condition had HEPES and PEG3350; perfluoropolyether was
> used as a cryoprotectant.
>
> We would appreciate any help in identifying it.​
>
> Thanks and regards,
>
> Uma.
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] To post to ccp4bb...

[CRAIG A BINGMAN]

A phospholipid headgroup might be rotationally disordered and washed out, 
especially if it isn’t exactly the correct binding partner.  It does look very 
much like lipid density to me. Attempts to model a diacyl glycerol and PEGs 
should be revealing.

On Jul 2, 2018, at 10:36 AM, Edward A. Berry 
mailto:ber...@upstate.edu>> wrote:

Is it a membrane protein?
Looks like a phospholipid without the phosphate. diglyceride maybe?
But I see not much blue density. Presumably this fills out if you contour
at a lower but still reasonable level?




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Postdoctoral Positions in Structural Biology – Maier Lab, Biozentrum, Basel, Switzerland

[Timm Maier]

The Maier Lab is looking to recruit postdoctoral scientists to study giant 
multienzymes, regulatory complexes and metabolic regulation.

We employ a combination of structural biology techniques, in particular 
cryo-EM, X-ray crystallography and XL-MS at state-of-the-art level to resolve 
the architecture of large protein assemblies. Additionally, we aim to visualize 
dynamics of multienzyme factories and transient regulatory interactions in 
eukaryotic cells.

For an overview of recent research in our team, cf. Science 351, 48-52 (2016), 
Nature 531, 533-537(2016); Nat Chem Biol 14, 474-479 (2018), Curr Opin Struct 
Biol 49, 177-189 (2018); Nature 558, 470-474 (2018). For more information, 
follow @MaierLab on Twitter or visit www.biozentrum.unibas.ch/maier.

Our group is embedded in the focal area “Structural Biology & Biophysics”, 
which offers a stimulating environment for interdisciplinary research. We 
collaborate intensely with teams in the areas of cellular signaling and 
infection biology. Excellent in-house facilities for electron microscopy, 
proteomics, imaging, biophysics, and large-scale computing support research and 
training.

We are looking for enthusiastic scientists who share our dedication to solving 
challenging problems in biology. Postdoc candidates should have obtained their 
PhD recently or expect to complete their PhD soon and are expected to have 
demonstrated their scientific excellence by at least one strong published or 
upcoming first author paper.

Ideal candidates are trained in state-of-the-art structural biology of large 
assemblies using cryo-EM or X-ray crystallography or have specific prior 
experience in mTOR signaling or polyketide synthase biology.  Experience in 
eukaryotic protein production, multi-scale modelling, super-resolution 
microscopy or single-molecule experiments is a plus.

The Biozentrum of the University of Basel is one of the leading institutes 
worldwide for molecular and biomedical basic research and teaching. It is home 
to more than 30 research groups with scientists from over 40 countries. 
Research at the Biozentrum focuses on the areas of Cell Growth & Development, 
Infection Biology, Neurobiology, Structural Biology & Biophysics and 
Computational & Systems Biology. With its more than 500 employees, the 
Biozentrum is the largest department at the University of Basel’s Faculty of 
Science. The Biozentrum is dedicated to excellence in research and education 
and provides outstanding training and career development support for Postdocs.

Basel is an international city with people from 150 nations. Located on the 
border where three countries meet - Switzerland-Germany-France -, it is 
Europe’s most important life sciences hub. Basel provides a high standard of 
living and a rich and varied cultural atmosphere.

Please visit www.biozentrum.unibas.ch/maier for more information and a link to 
the online application portal. Informal inquiries via e-mail to 
timm.ma...@unibas.ch are welcome.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] [ccp4bb] Oxford University Press

[Eugene Osipov]

AI researchers are boycotting Nature journals:
http://www.sciencemag.org/news/2018/05/why-are-ai-researchers-boycotting-new-nature-journal-and-shunning-others
May be there is something we can in our field?

2018-07-02 10:01 GMT+03:00 George Sheldrick :

> Since neither I nor my university can afford Elsevier journals, I have no
> access to papers published in them. In view of their excessive profits, for
> some years I have not submitted papers to them and have declined all
> requests to referee for them. If everyone did that, they might reconsider
> their approach. I am not an Apple fan either - I use a more reasonably
> priced native Linux laptop - but have to give Apple credit for innovation.
>
> George
>
>
>
> On 07/01/2018 06:57 PM, Patrick Loll wrote:
>
>
> I think what we should do is not publish in journal families where the
> profit is above 10 per cent. Elsevier is the place to start as their profit
> margins are like those of Apple, and of competition there is none.
>
>
> Elsevier: Like Apple, but without the design sense.
>
>
> But seriously, Adrian makes an excellent point. And the large profit
> margins wouldn’t be quite so galling, if only the publishers were able to
> provide competent and helpful administrative support; but in my recent
> experience, not-for-profit scientific society journals are actually
> providing better experiences for reviewers and authors than the big
> commercial ones.
>
> Pat
>
> 
> ---
>
> Patrick J. Loll, Ph. D.
>
> Professor of Biochemistry & Molecular Biology
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St
> .,
> Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
>
> pjl...@gmail.com
>
> pj...@drexel.edu
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-33021 or +49-5594-227312
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



-- 
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
Research Center of Biotechnology
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] To post to ccp4bb...

[Gerard Bricogne]

I would favour the PEG interpretations. PEG-y snakes like to nestle
against hydrophobic patches, and especially to lie on the large flat
indole rings of TRP side-chains (like this one does).

Gerard.

--
On Mon, Jul 02, 2018 at 04:01:29PM +0100, Eleanor Dodson wrote:
> Looks Pegy...
> 
> 
> On 2 July 2018 at 15:30, Artem Evdokimov  wrote:
> 
> > PEG snake or possibly a short, very disordered peptide (or several
> > peptides occupying the same density).
> >
> > Artem
> >
> > - Cosmic Cats approve of this message
> >
> > On Mon, Jul 2, 2018 at 6:26 AM, Christopher Horne  > canterbury.ac.nz> wrote:
> >
> >> Does anyone have any insight into this weird density?
> >>
> >> Present at dimer interface, PEG in condition. I have seen a previous post
> >> which mentions "PEGs can create ugly "snakes" of variable density that
> >> may be challenging to model".
> >>
> >>
> >>
> >> This email may be confidential and subject to legal privilege, it may
> >> not reflect the views of the University of Canterbury, and it is not
> >> guaranteed to be virus free. If you are not an intended recipient,
> >> please notify the sender immediately and erase all copies of the message
> >> and any attachments.
> >>
> >> Please refer to http://www.canterbury.ac.nz/its/email-disclaimer/  for more
> >> information.
> >>
> >>
> >> --
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >>
> >
> >
> > --
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] To post to ccp4bb...

[Edward A. Berry]

Is it a membrane protein?
Looks like a phospholipid without the phosphate. diglyceride maybe?
But I see not much blue density. Presumably this fills out if you contour
at a lower but still reasonable level?

On 07/02/2018 06:26 AM, Christopher Horne wrote:

Does anyone have any insight into this weird density?

Present at dimer interface, PEG in condition. I have seen a previous post which mentions "PEGs 
can create ugly "snakes" of variable density that may be challenging to model".



This email may be confidential and subject to legal privilege, it may
not reflect the views of the University of Canterbury, and it is not
guaranteed to be virus free. If you are not an intended recipient,
please notify the sender immediately and erase all copies of the message
and any attachments.

Please refer to http://www.canterbury.ac.nz/its/email-disclaimer/ for more
information.


--

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Postdoctoral position at EMBL in Hamburg

[Victor Lamzin]

Dear Colleagues,

We are looking for a highly motivated Postdoctoral researcher to join 
our efforts in structure-based search of new drug leads. If you have 
experience in macromolecular crystallography, sample preparation and 
scientific programming, and interested in this position, please refer to 
the job description and application instructions at:


https://www.embl-hamburg.de/jobs/searchjobs/index.php?ref=HH_00144

The closing date for applications is 12th August 2018.

With best regards,
Victor Lamzin




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] ERC-funded Post-Doctoral and PhD positions available

[Gros, P. (Piet)]

Two 2.5-year ERC-funded post-doctoral positions and one 4-year PhD student 
positions are currently available in the group of Piet Gros on structural, 
biophysical and biochemical studies of the human complement system.

I am looking for highly motivated and talented researchers. Post-doc candidates 
with proven expertise in structural biology/protein biochemistry (PD1) or 
membrane biology/lipid biochemistry (PD2) are asked to apply. Candidates for 
the PhD position must have a MSc degree in molecular life science, 
(bio)chemistry, biophysics or (molecular and cellular) biology.

The Bijvoet Center Biomolecular Research at the Utrecht University offers a 
collaborative environment and state-of-the-art infrastructure (e.g. EM, MS, 
light microscopy, protein and membrane biochemistry). Cryo-EM microscopes are 
available at the Utrecht EM-square and national facility NeCEN.

You are asked to send in an application consisting of a CV, a motivation letter 
and two references, no later than August 23rd 2018 to 
science.secr...@uu.nl

Piet Gros
Bijvoet Center for Biomolecular Research
Utrecht University, Netherlands
www.uu.nl/staff/PGros/0
www.crystal.chem.uu.nl/~gros/frontpage.php






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Application Deadline Tomorrow - Postdoc Position at Imperial College London

[Zhang, Xiaodong]

Dear all,

We invite enthusiastic individuals to apply for a Research Association position 
in the group of Xiaodong Zhang 
(https://www.structurebiomed.org), within the 
Section of Structural 
Biology,
 Department of Medicine, at Imperial College London’s South Kensington Campus.

The successful candidate will join a multi-disciplinary team of international 
researchers investigating the structures and mechanisms of bacterial 
transcription regulation and signal transduction by AAA ATPases. We employ a 
combination of Biochemistry, cryo electron microscopy and X-ray 
crystallography, utilizing our excellent protein production and structural 
biology facilities at Imperial.

We welcome individuals with a PhD (or about to obtain one) in structural 
biology, biochemistry or biophysics with a strong interest in 
inter-disciplinary structural molecular biology research.

The post is full-time for up to 48 months.

Application deadline: July 3rd, 2018

For details and application procedure, please visit 
https://www.imperial.ac.uk/jobs/description/MED00558/research-associate

 For informal enquiries, please contact: 
xiaodong.zh...@imperial.ac.uk

Prof Xiaodong Zhang
Section of Structural Biology
Department of Medicine
Imperial College London

Room 104, Sir Alexander Fleming Building
South Kensington, SW7 2AZ
xiaodong.zh...@imperial.ac.uk
http://www.imperial.ac.uk/people/xiaodong.zhang
(0) 207 594 3151

PA - Ms Sorina Damsa, structuralbiolog...@imperial.ac.uk, (0) 207 594 2917




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] [ccp4bb] Oxford University Press

[George Sheldrick]

Since neither I nor my university can afford Elsevier journals, I have 
no access to papers published in them. In view of their excessive 
profits, for some years I have not submitted papers to them and have 
declined all requests to referee for them. If everyone did that, they 
might reconsider their approach. I am not an Apple fan either - I use a 
more reasonably priced native Linux laptop - but have to give Apple 
credit for innovation.


George


On 07/01/2018 06:57 PM, Patrick Loll wrote:


I think what we should do is not publish in journal families where 
the profit is above 10 per cent. Elsevier is the place to start as 
their profit margins are like those of Apple, and of competition 
there is none.


Elsevier: Like Apple, but without the design sense.


But seriously, Adrian makes an excellent point. And the large profit 
margins wouldn’t be quite so galling, if only the publishers were able 
to provide competent and helpful administrative support; but in my 
recent experience, not-for-profit scientific society journals are 
actually providing better experiences for reviewers and authors than 
the big commercial ones.


Pat

---

Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology

Drexel University College of Medicine

Room 10-102 New College Building

245 N. 15th St., Mailstop 497

Philadelphia, PA19102-1192USA


(215) 762-7706

pjl...@gmail.com 

pj...@drexel.edu 





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 






--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1