Re: [ccp4bb] Problem with Mg2+ binding site refinement

[Prem Prakash]

Hi Mubinur,
I got the same situation while refining my protein complex with Lanthanum
ion complex, reducing the occupancy while refining solved the problem.
Good luck
P.P

On Thu, Jun 15, 2017 at 11:17 PM, Pavel Afonine  wrote:

> Hi Mubinur,
>
> try without "metal restraints" and see if that helps. As others suggested,
> make sure 2+ is present in rightmost column of PDB file. The side may be
> partially occupied, so refining occupancy of Mg2+ is not a bad idea.
>
> Pavel
>
> On Wed, Jun 14, 2017 at 2:44 PM, Mohammad Rahman 
> wrote:
>
>> Dear All,
>>
>> I am trying to refine a tetrameric enzyme structure that was determined
>> at 2.7 Å. The structure contains a Mg2+  binding site in each monomer.
>> After refinement,   in Mg2+ binding site  negative density (red) has been
>> found as in pictures. I am using Phenix refine, and during refinement,
>> metal restrains were used. Herewith I have attached the refinement
>> statistics.
>>
>> please help me to overcome this problem.
>>
>> Thank you
>>
>> -Mubinur
>>
>>

[ccp4bb] Post-doctoral position at Academia Sinica in Taipei, Taiwan

[godzella]

We are looking for a highly qualified and motivated postdoctoral researcher
with a strong background in X-ray crystallography, molecular biology or
biophysics. We work on biochemical and structural studies of various
RNA-binding proteins, RNases and helicases involved in RNA metabolism (see
our web site: http://hyuan.imb.sinica.edu.tw/ ).

 

Please send applications (including CV, research experience, and at least
two names and contact information for references) by email to:

Professor Hanna S. Yuan

Email: ha...@sinica.edu.tw

Institute of Molecular Biology

Academia Sinica, Taipei, Taiwan

Re: [ccp4bb] Problem with Mg2+ binding site refinement

[Pavel Afonine]

Hi Mubinur,

try without "metal restraints" and see if that helps. As others suggested,
make sure 2+ is present in rightmost column of PDB file. The side may be
partially occupied, so refining occupancy of Mg2+ is not a bad idea.

Pavel

On Wed, Jun 14, 2017 at 2:44 PM, Mohammad Rahman 
wrote:

> Dear All,
>
> I am trying to refine a tetrameric enzyme structure that was determined at
> 2.7 Å. The structure contains a Mg2+  binding site in each monomer.  After
> refinement,   in Mg2+ binding site  negative density (red) has been found
> as in pictures. I am using Phenix refine, and during refinement, metal
> restrains were used. Herewith I have attached the refinement statistics.
>
> please help me to overcome this problem.
>
> Thank you
>
> -Mubinur
>
>

[ccp4bb] Senior Structural Scientist Position at Merck Research Laboratories

[Soisson, Stephen M]

I would like to alert the community to an opportunity at Merck Research 
Laboratories.  Please do not respond  directly to me, all applications must be 
done through the online system at the link below:

https://taleo.msd.com/careersection/merck_external_career_section/jobdetail.ftl?job=RES001892=en_id=mailto#.WUGmK92NpuI.mailto
Thanks!

Steve Soisson

Membrane Protein Structural Scientist - Chemistry, Capabilities and 
Screening-RES001892

Description



Merck Research Laboratories South San Francisco, a wholly owned subsidiary of 
Merck and Co., is focused on driving discovery research.  Our new 
multi-disciplinary discovery research site offers state-of- the-art resources 
to explore the most promising science combined with Merck's world-class R 
expertise in small molecules and biologics. Located within the heart of the Bay 
area's biomedical community, research conducted in our new laboratories spans 
exploratory biology through early clinical development and is an integral part 
of Merck's powerful world-class network of drug and vaccine discovery.



At Merck, we are inspired by the belief that a research-driven enterprise 
dedicated to scientific excellence can create medicines and vaccines that save 
and improve lives. Every employee is building on our proud legacy of scientific 
breakthrough. Our ability to impact the lives of patients worldwide depends on 
the integrity, creativity, humility and scientific acumen of our team. We are 
creating a diverse organization that is inspired by invention and founded on a 
culture of respect and collaboration. At Merck Research Labs South San 
Francisco, you'll have the opportunity to expand your knowledge and skills 
through collaboration with talented and dedicated colleagues while advancing 
your career.



Location:

This position will be based in West Point, PA for the first 12-18 months and 
then permanently transition to South San Francisco upon completion of 
construction of this new Merck site.  The ability to accommodate these location 
requirements is essential.



This position within the Chemistry, Capabilities and Screening group at Merck 
Research Laboratories will support drug lead discovery and optimization through 
the experimental structural determination and interpretation of therapeutically 
important targets.

* The successful candidate will perform crystallization screening, 
crystal optimization, and structure determination of ligand complexes and will 
work in collaboration with medicinal and computational chemists

* Work closely with molecular biologists and protein biochemists and 
will have access to automated cloning, expression, and crystallization 
technologies as well as a variety of instrumentation for biophysical analyses

* Productive and collaborative interactions with other members of the 
global, cross-functional department

* Cooperative and collaborative use of internal expertise and resources 
will be essential to success

* The position requires active interaction with the external scientific 
community to continually improve scientific understanding, including 
presentations at national or international meetings

Responsibilities include and are not limited to the following:

* Support drug lead discovery and optimization through the 
determination of X-ray structures of therapeutically important targets with a 
focus on membrane proteins.

* Perform crystallization, crystal optimization, and structure 
determination of protein-ligand complexes to drive structure-based drug 
discovery

* Productive and collaborative interactions with other members of the 
cross-functional department, including medicinal and computational chemists, 
biochemists, and molecular biologists. Cooperative and collaborative use of 
internal expertise will be essential to success

* Active interaction with the scientific community to continually 
improve scientific understanding, including presentations at national or 
international meetings and publication in peer-reviewed journals

* Active participation in recruitment, training and development of 
scientific staff

* Periodic travel to other locations will be required

Consistently cited as an inspiring place to work, Merck employs talented people 
who discover, develop, manufacture, and market a wide range of vaccines and 
medicines to address unmet medical needs. Each of us is joined by an 
extraordinary sense of purpose bringing Merck's finest achievements to people 
worldwide.





Qualifications



Education / Work Experience :

* Required:  Ph.D. degree with a minimum of (8) years experience in 
Membrane Protein Structure Determination

Required Experience:

* Minimum of (8) years experience in the application of Structural 
Biology to Industrial Drug Discovery

* Proven track record in the use of state-of-the-art  membrane protein 
structural biology techniques, 

[ccp4bb] CCP4 website

[Engin Özkan]

Hi,

I am unable to reach the CCP4 website and the CCP4 online services 
regularly. The websites appear to be down (for everyone) on and off. 
Could we alert someone responsible to look into this?


Thank you,

Engin

Re: [ccp4bb] Shape similarity of ligand binding sites

[Robert Campbell]

Hi Stephen,

I have a python script that does exactly that.  It uses a surface calculated by 
MSMS and calculates the similarity using a function like that of the SC 
program.  You'll need to align the structures first.  There is an equivalent 
script that calculates the complementarity of two surfaces.  I also have a 
script that reads the output of this and draws the surface in PyMOL and colours 
it according to the SC value at each vertex.

You can find the similarity and complementarity scripts here, along with some 
instructions:

  http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/#msms_similarity.py
  
http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/#msms_complementarity.py

The script for drawing the surface is here:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/#msms_sim_draw.py


Cheers,
Rob


On Wed, 2017-06-14 11:42  +,  "" 
 wrote:

> Dear ccp4bb,
> 
> I am trying to compare the shape of a ligand binding site in my
> protein with that of some homologues and mutants and was wondering
> how others go about this?  I specifically want to compare the shapes
> of the surface (similar to an sc analysis of an interface) rather
> than the positions of the atoms in the residues that make up the
> site.  I have come across PESDserv, but this doesn't do quite what I
> would like.  Any suggestions would be very welcome.
> 
> Best wishes,
> 
> Steve
> 
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email stephen.c...@rc-harwell.ac.uk
> tel 01235 567717
> 
> This email and any attachments may contain confidential, copyright
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-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

[ccp4bb] PhD position - Phytochrome structure/function

[Hughes, Jon]

Dear collegues, I would be grateful if you were to draw the attention of 
appropriate persons to the following flyer (if the fancy html formatting 
doesn't work, here's the flyer in PDF:
http://www.uni-giessen.de/fbz/fb08/Inst/pflphys/pflaphygroups/ag-hughes/PositionsAvailable/resolveuid/402bc6a30e8e41bca6e50d12d745062b
With many thanks in advance and best wishes, Jon.



[jlu_logo_homepage] 
[cid:image004.png@01D2E5D7.699138E0]

PhD position: Phytochrome structure/function

A PhD position at the Institute for Plant Physiology of the Justus Liebig 
University is available immediately. The position (E13 66%) is funded for three 
years by the DFG as part of Sfb1078 (Protonation Dynamics in Protein Function; 
see www.sfb1078.de) in Berlin.
The aim of the project is to derive an understanding of the functional 
mechanism underlying photoconversion and signal activation in the phytochrome 
family of photoreceptors. To this end we will use both X-ray and neutron 
crystallography to study structural changes associated with photoconversion in 
various phytochromes. The work is augmented by long-standing co-operations with 
vibrational spectroscopy and MAS NMR groups in Berlin and Leipzig and has 
already lead to numerous prominent publications. The successful candidate will 
work with Dr. Soshi Nagano to create appropriate derivatives of both 
prokaryotic as well as plant phytochromes for crystallisation and structural 
determination at the atomic level. The work will include visits to various 
international research facilities and extensive personal interactions with 
other members of the Berlin Sfb. We have access to advanced robotic facilities 
to assist us in screening for appropriate crystallisation conditions.

The candidate should have graduated in biochemistry, molecular biology or a 
related field. Experience in protein biochemistry and/or physicochemical 
analysis of protein structure/function or would be an advantage. Proficiency in 
written and spoken English and ability to work constructively in a 
multinational, interdisciplinary team is important. Applications from women and 
disabled persons are especially welcome.

If you are interested, please apply immediately by e-mail including a tabular 
CV:  Professor Jon Hughes, Plant Physiology, JLU Giessen, Germany 
(jon.hug...@uni-giessen.de).

For further details see 
www.uni-giessen.de/fbz/fb08/Inst/pflphys/pflaphygroups/ag-hughes

[ccp4bb] PDBe Software Engineer / Bioinformatician

[John Berrisford]

Dear CCP4BB

PDBe are looking for a software engineer to develop data integration 
pipelines for disparate data sources (all co-located at the EBI) and Web 
components for visualization of this integrated data. In addition, the 
project will involve creation of REST API calls to make this data 
available for the scientific community.


For more details and to apply, please see the listing on the EMBL 
careers site 
(https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj=55746=15470)



The deadline for applications is the 9th July 2017.

Thanks

John

--

John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

http://www.pdbe.org
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope