[ccp4bb] 46th National Seminar on Crystallography, 27-29 June 2018, Bangalore, India

[Padmanabhan B]

Dear All, 

Wishing you all A Happy & Prosperous New Year, 2018!

 We are delighted to announce the upcoming "46th National Seminar 
on Crystallography" to be held on June 27-29th, 2018 at National Institute of 
Mental Health and Neurosciences (NIMHANS), Bangalore, India. The main symposium 
will consist of a comprehensive scientific program including Prof. M. Vijayan 
lecture. We are expecting a huge turnout of audience from academics, research 
as well as industry.
Our website (NSC46 Website 
) is up and running. The preliminary 
program with all the necessary registration information will be available on 
the given website. This website will be dynamically updated in a periodic 
fashion, with information about speakers, sponsors and other details, as the 
weeks roll by. An important aim of this conference is to offer networking 
opportunities and foster debate among hundreds of participants from all over 
India. Through your participation, you can help developing issues to be 
explored further by crystallographers and generate novel methodologies to 
address the former issues.

Keep tracking for latest updates on our website. We are looking forward to see 
you at NSC46.

Best Wishes,
Convener
Prof. B. Padmanabhan, Ph.D
Professor & Head
Department of Biophysics
National Institute of Mental Health and Neuro sciences (NIMHANS)
Bangalore - 560029 
India
Email: nsc46.in...@gmail.com; balapa...@gmail.com

Re: [ccp4bb] Research Specialist II Position Opportunity at Cedars-Sinai Inflammatory Bowel and Immunobiology Research Institute (IBIRI), Los Angeles, CA

[Velasco, Christy]

The Cedars -Sinai F. Widjaja Foundation Inflammatory Bowel and Immunobiology 
Research Institute (IBIRI) is searching for a highly motivated Research 
Specialist II to be part of Cedars-Sinai's commitment to Precision Health 
through an exciting opportunity within our IBD Drug Discovery and Development 
Unit (IBD3). We are a multidisciplinary basic, translational and clinical 
program devoted to mucosal inflammation. The mission of the IBD3 unit is to use 
personalized medicine approaches to predict the success of current and future 
therapeutic for inflammatory bowel diseases. The IBD3 program is u uniquely 
structured to join academic science with industry partners to discover and 
validate new therapeutic targets, accelerate drug development through patient 
stratification, and rescue and repurpose failed drugs by identifying drug 
responsive patient populations. The unit embodies a spirit of discovery with 
world leaders and research scientists on the care and management of IBD.



More information can be found at: 
https://www.cedars-sinai.edu/Research/Research-Labs/Bilsborough-Lab/



The IBD3 unit is seeking a mission-focused Research Specialist II, with the 
expertise in the development of protein expression and purification strategies 
to support ongoing drug discovery and development needs. Under the leadership 
of the IBD3 unit Director, the Research Specialist II will utilize a solid 
foundation in research and experience with techniques associated with a 
specific area of research.  Incumbent will be capable of exercising independent 
judgment while developing and implementing research programs, project planning, 
enrollment of patients, experimental protocols and procedures, database 
development and analysis including evaluating and interpreting results.  Will 
supervise lab activities, including research grant management, human resources, 
responsibility delegation, and provide training to other individuals who may be 
assigned to the project, study, or laboratory.  Reports to and works closely 
with Principal Investigator and has independent supervision of a laboratory or 
program.  Will prepare grant proposals, publications, and presentations. Will 
function as a bridge between research and clinical programs which may have 
local and national contributors and investigators relying on information 
provided.  Will have delegated authority to make substantive decisions and 
commitments in accord with the established goals and objectives of the 
laboratory or program.



Essential Job Duties and Responsibilities:



- Acts as a project lead and coordinator interacting with collaborators, 
clinical research personnel and researchers as part of a research team.

- Participates in all aspects of clinical development and study management 
(protocol design, enrollment of patients, development and implementation of 
protocols, and if applicable, submission of IRB applications and approvals).

- Follows established procedures or protocols to perform laboratory tests 
and/or experiments which will include: basic tissue culture, immunoassays, 
molecular biology techniques, microscopy, animal preparation (e.g. tail vein 
injections) and surgery.

- Provides scientific expertise to ongoing and future trials.

Identify and resolve common problems involved in routine research assays.

- Establishes and maintains relationships with clinical investigators and 
manages internal and external collaborative research projects.

- Acts as a scientific resource for the affiliated pre-clinical research 
laboratory (e.g., assisted with experimental designs, data analysis, 
interpretation of scientific literature).

- Supervises, leads, and trains other individuals assigned to the lab.

- Prepares grant applications and oversees submission process, including 
writing of grant proposal.

- Capable of exercising independent judgment while participating in the 
planning of experiments and evaluating and interpreting results.

- Operates appropriate laboratory equipment.

- Monitors inventory levels, orders materials and supplies in accordance with 
established policies and procedures.

- Operates lab computers for data entry and maintains accurate data records.

- Uses various software applications, such as spreadsheets, electronic mail, 
World Wide Web, statistical packages, and graphics packages to assemble, 
manipulate and/or format data and/or test reports.



Department and/or Unit Specific:



- Must demonstrate strong biochemistry skills and keeps up-to-date with the 
latest technologies to continually improve operational procedures.

- Able to Implement a variety of expression systems including e.coli, mammalian 
and baculovirus cell culture

- Hands on expertise in construct design, protein expression and purification

- Proven experience in difficult-to-express and purify proteins such as 
membrane proteins, enzymes and Fc-fusion for biologics, X-ray crystallography 
andcryo-EM

- Works closely with comput

[ccp4bb] New Post-doc Positions at Ohio State

[Andrew Reed]

Dear All,

I am posting a new job vacancy on behalf of Dr. Zucai Suo. Below is the 
description of the job and applicant requirements. Please contact Dr. Suo 
directly with any questions or applications.

Two postdoctoral positions are available immediately in Dr. Zucai Suo’s 
laboratory tostudy substitution errors of DNA replication, DNA replication fork 
reconstitution, enzymatic functions, mechanisms, and enzyme-substrate 
interactions through time-dependent and conventional X-ray crystallography as 
well as single particle Cryo-electron microscopy. Protein targets for these 
studies are various DNA or RNA polymreases and gene editing enzymes. The ideal 
candidate should have a PhD in structural biology and extensive experience in 
all aspects of protein X-ray crystallography, including protein expression and 
purification, crystallization, structure determination and refinement. 
Experience with baculovirus/insect cells expression system and Cryo-EM is a 
plus. Please contact Dr. Suo through email at su...@osu.edu, phone (614) 
688-3706, or regular mail: 880 Bio. Sci., 484 West 12th Ave., Department of 
Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210.

Best,

Andrew Reed
Pelotonia Fellow, Co-Lab Manager
Ph. D. Candidate, Zucai Suo Lab
Ohio State Biochemistry Program
Room 584, Biological Sciences Building
484 W. 12th Ave., Columbus, OH 43210
(614)-292-1590

[ccp4bb] 2018 Gordon Research Conference on Ligand Recognition & Molecular Gating

[C. Thangaratnarajah]

Dear all,

this is sent on behalf of Edmund Kunji:

As Chairs, it is our pleasure to invite you to the *2018 Gordon Research 
Conference* on *Ligand Recognition & Molecular Gating*, which will be 
held in Ventura Beach Marriott, Ventura, 4-9 March 2018. The principle 
goal of this GRC is to share the latest knowledge and expertise on the 
mechanism and function of G-protein coupled receptors, transporters, and 
ion channels. The conference is preceded by the Gordon Research Seminar 
on the same topic, which will give opportunities to young scientists to 
present their work. We have invited a fantastic list of speakers and 
there are still a large number of poster presentations available. The 
website with more information can be found here: 
https://www.grc.org/ligand-recognition-and-molecular-gating-conference/2018/


Best wishes,

Edmund Kunji and Alessio Accardi

*
*

*I**nvited speakers *

Eric Gouaux



Janice Robertson



Ali Jazayeri

Nieng Yan



Ming Zhou



Brian Kobilka

Kurt Wüthrich



Henry Colecraft



Lily Jan

Cristina Paulino



Richard Hite



Amy Newman

Raimund Dutzler



Crina Nimigean



Hoangdung Ho

Mei Hong



Bonnie Wallace



Randy Stockbridge

Jian Yang



Liz Carpenter



Ronald Kaback

Irina Serysheva



Poul Nissen



David Drew

Jian Yang



Zhe Zhang



Joanne Parker

Hartmut Luecke



Kaspar Locher



Tetiana Serdiuk

Kaspar Locher



Daniel Oprian



Osamu Nureki

Lucy Forrest



Patrick Sexton



Simon Newstead

Simon Scheuring



Roger Sunahara



John Walker

[ccp4bb] 2018 Gordon Research Conference on Ligand Recognition & Molecular Gating

[C. Thangaratnarajah]

Dear all,

this is sent on behalf of Edmund Kunji:

As Chairs, it is our pleasure to invite you to the *2018 Gordon Research 
Conference* on *Ligand Recognition & Molecular Gating*, which will be 
held in Ventura Beach Marriott, Ventura, 4-9 March 2018. The principle 
goal of this GRC is to share the latest knowledge and expertise on the 
mechanism and function of G-protein coupled receptors, transporters, and 
ion channels. The conference is preceded by the Gordon Research Seminar 
on the same topic, which will give opportunities to young scientists to 
present their work. We have invited a fantastic list of speakers and 
there are still a large number of poster presentations available. The 
website with more information can be found here: 
https://www.grc.org/ligand-recognition-and-molecular-gating-conference/2018/


Best wishes,

Edmund Kunji and Alessio Accardi

*
*

*I**nvited speakers *

Eric Gouaux



Janice Robertson



Ali Jazayeri

Nieng Yan



Ming Zhou



Brian Kobilka

Kurt Wüthrich



Henry Colecraft



Lily Jan

Cristina Paulino



Richard Hite



Amy Newman

Raimund Dutzler



Crina Nimigean



Hoangdung Ho

Mei Hong



Bonnie Wallace



Randy Stockbridge

Jian Yang



Liz Carpenter



Ronald Kaback

Irina Serysheva



Poul Nissen



David Drew

Jian Yang



Zhe Zhang



Joanne Parker

Hartmut Luecke



Kaspar Locher



Tetiana Serdiuk

Kaspar Locher



Daniel Oprian



Osamu Nureki

Lucy Forrest



Patrick Sexton



Simon Newstead

Simon Scheuring



Roger Sunahara



John Walker

[ccp4bb] Postdoc position at OSU

[McElroy, Craig]

The McElroy laboratory in the College of Pharmacy at the Ohio State University 
is seeking a postdoctoral researcher in structural biology to support multiple 
drug discovery research projects.
Qualifications:

* Ph.D. in Biochemistry, Molecular Biology, Structural Biology, or a 
related field

* Experience with cloning, high-level protein overexpression, and 
protein purification methods is required

* Experience in the methods and approaches for macromolecular 
crystallography is preferred

* Ability to plan and execute research projects independently and meet 
project deadlines is required

* Excellent problem solving, interpersonal, communication, and 
presentation skills
Responsibilities include:

* Performing experiments for cloning/subcloning, protein expression, 
and purification of proteins for biochemical and structural studies; 
crystallization; optimizing crystallization conditions; and collecting and 
analyzing diffraction data.

* Performing model building and structure refinement.

* Maintaining laboratory supplies and equipment to meet the needs of 
research activities

* Assisting with preparation of grant proposals, presentations, and 
publications

The Ohio State University is well equipped with state-of-the-art equipment for 
molecular biology, protein purification, and crystallography, including a 
Mosquito crystallization robot and Rigaku X-ray generator. Please address 
questions to mcelroy...@osu.edu and apply at 
https://www.jobsatosu.com/postings/83593.

Best Regards,
Craig

[The Ohio State University]
Craig McElroy, PhD
College of Pharmacy
345 Parks Hall | 500 W. 12th Ave. Columbus, OH 43210
614-292-3232 Office
mcelroy...@osu.edu  osu.edu
mcel...@pharmacy.ohio-state.edu  
pharmacy.osu.edu

[ccp4bb] XSEED Conference 2018

[Balendu Avvaru]

Dear all,

Please check out the new XSEED 2018 Conference in the beautiful German town of 
Heidelberg. It is a 2-day event where scientists from both academia and 
industry will bridge the gap between the two worlds. The event offers 
cross-pollination between researchers from distinct disciplines 
(nanotechnology, bioinformatics, genetics, biophysics, cell biology) to go 
beyond the current boundaries in biomedical research, and to plant intellectual 
seeds about future technologies in the minds of all participants. Early bird 
registration ends on February 15th, 2018. Click on the link below for more 
details.

http://xseed-conference.com/

Best wishes,
Balendu

--
Balendu Avvaru, PhD
Group Leader
 BioMed X Innovation Center
m Neuenheimer Feld 515
69120 Heidelberg, Germany
www.bio.mx

Re: [ccp4bb] 3D stereo and pymol

[David Schuller]

The Mate desktop should also work; it is a continuation of the old Gnome 
2 desktop.


- dave schuller

On 01/03/18 04:42, Wim Burmeister wrote:
I answer a bit late, but I repost a message on 3D graphics from Mai 
2017 :


Hello,

we just wanted to share our experience in finding a configuration 
which allows to use 3D graphics under linux using Nvidia GeForce 3D 
glasses.


We had quite a hard time to find a configurations which works correctly.

We finally used Debian linux with a xfce desktop. Other recent 
desktops use a tiling which is not compatible with 3D graphics.


The hardware consists of

  * a DELL Precision T5810 desktop computer with an Nvidia Quadro
M4000 (8 Gbyte memory, 4 DP) graphics card
  * Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
active stereo glasses
  * a stereo connector PNY Quadro 4000 3D for the synchronization of
graphics card and glasses
  * an ASUS 24" LED 3D - VG248QE display
  * a DisplayPort-DisplayPort cable

The Nvidia linux drivers from version 367.57 can handle the current 
version of the Nvidia glasses.


For an obscure reason a direct DP-DP connection between graphics card 
and display is absolutely required in order to obtain fully working 
stereo. If a DP-DVI dual link adapter is used, the stereo does not 
work on the top and the bottom part of the screen. This is true for a 
native DELL active adaptor or generic models. The exact reason remains 
unresolved, but the solution is to use a direct DP-DP connection. This 
limits the available choice of displays which require 120 Hz for 
1080*1980 screen resolution and a DP input. We have been choosing a 
“Nvidia 3D ready” model.


There has been a considerate about of exchange about this problem on

https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/

The setup comes with a price tag of about 1600 € free of taxes.

coot, pymol and chimera work straight without problems in hardware 
stereo mode. The experience is absolutely great.


Best

Wim

--

Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs

CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website 



//



--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

[Kabasakal, Burak V]

In our acetone carboxylase structure, the active metal site contains a 
octahedral Mn coordinated with two His, one Asp, and one Glu residues. It looks 
very similar.

https://www.nature.com/articles/s41598-017-06973-8

The protein may have a metal in the active site, is there any background 
information? Or the metal has bound adventitiously, to find out more anomalous 
data collection is required, like other people said.

Burak

From: CCP4 bulletin board  on behalf of Goldman, Adrian 

Sent: 29 December 2017 20:32:34
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

All true, I did my undergraduate thesis (at cambridge about 10**6 years ago it 
feels) on the formation of carboxylate-pairs in the gas phase….  But I agree 
with the thread: there is a metal there; it’s almost certainly not Mg, but it’s 
hard to say without further data whether its Mn, Fe, Cu, Zn - those being the 
most likely culprits.  Someone suggested that scanning the edges might tell, 
and I agree.  But what he might find is a mixture, as the metal is probably 
adventitious and has just been picked up, possibly from whatever is present in 
solution.  We’ve had that experience.

Adrian


On 29 Dec 2017, at 17:31, Tristan Croll 
mailto:ti...@cam.ac.uk>> wrote:

In this case, yes - there’s clearly a metal ion coordinated there. But for the 
record, it is entirely possible (if somewhat rare) to get acidic side chains 
directly contacting each other. Look up “carboxyl-carboxylate pair”. They’re 
typically found at low pH and/or in quite protected environments. Think of it 
as having one carboxyl group protonated and H-bonding to the other, except that 
the proton is more-or-less equally shared. Their most common role is as 
pH-dependent conformational switches - very stably bonded below the pKa, 
wanting nothing to with each other above.



Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY




On 29 Dec 2017, at 14:18, Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:

Hi Anurag,

There is a metal in the middle there. You need to figure out which one. Have a 
look at the crystallization conditions. If can also have a look at anomalous 
signal.

Cheers,
Robbie

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anurag 
Misra
Sent: Friday, December 29, 2017 14:55
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

Dear all,
I have solved a protein structure at 2.8 A resolution with Rfree 26%. In this 
structure catalytic His interacts with non catalytic Asp. This His-Asp pair 
(Chain A) is facing another identical His-Asp pair (in Chain B) which are 
related with 2-fold ncs (pics are attached) (The molecule exists as a dimer). 
There is another His-Asp pair in chain C (not shown in attached pic) which 
faces to the identical pair related to crystallographic 2-fold. (min distance 
Asp-Asp 2.58 A, His-His 3.6 A and His1-Asp1/His1-Asp2 ~3.0 A)
How to explain Asp-Asp head on pairs in close proximity? Is there a role of His 
in making such pairs. Is there any role of change in pKa to allow such 
interactions? Kindly suggest a few references where similar Asp-Asp pairs have 
been seen.

I appreciate your kind attention.
Thank you so much for helping me.
Best regards,
Anurag

Re: [ccp4bb] Dear All

[Amit Meir]

Dear Amala,
1. Increase your buffer pH. As a rule of thumb, usually it is 
recommended to work with pH 7.6 and above for Ni purification. Try pH 8.
2. Increase your buffer A [NaCl] to 500mM. Some proteins are more stable 
in higher NaCl, and for many, 50mM is not enough. It is possible your 
protein has already precipitated in the lower [NaCl]. You can also 
increase glycerol to 10%.


Having said that, you didn't provide additional details (Protein's 
origin - eukaryotic/ prokaryotic) - if it's from a eukaryotic source, it 
could be your protein needs additional post translation modifications 
(e.g. sugars etc) for stabilization, which most likely will require a 
different expression system. If your protein is of a bacterial source, I 
would try to add a solubility tag (eg MBP), change the location of the 
His tag, or change expression conditions (lower temp, different strain).

There are plenty of other options, but I'd start with that.

Good luck,
Amit



On 03/01/2018, 05:56, amala mathimaran wrote:


I am trying to purify a protein using HIS-select Ni-affinity column 
(washing with 50mM Tris pH7.5, 50mM NaCl, 30mM imidazole, 3mM BME, 
5%glycerol and elution with the same buffer + 250mM imidazole, 500mM 
Nacl). The protein (pI= 6.04) becomes cloudy/precipitated within 
15minutes of after elution. I add EDTA to the eluted protein 
immediately in the fraction tubes but the protein still precipitate, 
can anyone suggest how to avoid precipitation of protein.



Thanks and Regards,




--
*
Dr. Amit Meir
Professor Gabriel Waksman's group
Institute of Structural and Molecular Biology
Department of Biological Sciences
Birkbeck College
Malet Street
London WC1E 7HX
UK

[ccp4bb] Postdoctoral position at EMBL Grenoble

[Kowalinski Eva]

Dear colleagues,

a postdoctoral position is available in the lab of Dr. Eva Kowalinski at the 
EMBL Grenoble, France. We are looking for a highly motivated and ambitious 
individual to join investigations into the structure and function of large 
RNA-protein complexes. We will use a multidisciplinary approach to tackle 
complex biochemical problems by combining cryo-EM, X-ray crystallography and 
other biochemical and biophysical methods.

Details and application:
https://www.embl.de/jobs/searchjobs/index.php?ref=GR_00114 


Please share,
Eva Kowalinski



Dr. Eva Kowalinski
Group Leader

EMBL Grenoble,71 Avenue des Martyrs, 38042 Grenoble Cedex 09, France

T +33 476 20 74 46

Re: [ccp4bb] 3D stereo and pymol

[Wim Burmeister]

  
  
I answer a bit late, but I repost a message on 3D graphics from Mai
2017 : 

Hello,
 
we just wanted to share our experience in finding
  a configuration which allows to use 3D graphics under linux
  using Nvidia GeForce 3D glasses.
 
We had quite a hard time to find a configurations
  which works correctly.
 
We finally used Debian linux with a xfce desktop.
  Other recent desktops use a tiling which is not compatible
  with 3D graphics.
 
The hardware consists of

  a DELL Precision T5810 
  desktop computer with an Nvidia Quadro M4000 (8 Gbyte memory,
  4 DP) graphics card
  Nvidia
  GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
  active stereo glasses
  a stereo
  connector PNY Quadro 4000 3D for the synchronization of
  graphics card and glasses
  an ASUS 24"
  LED 3D - VG248QE display
  a
  DisplayPort-DisplayPort cable


The Nvidia linux drivers from version 367.57 can
  handle the current version of the Nvidia glasses.
 
For an obscure reason a direct DP-DP connection
  between graphics card and display is absolutely required in
  order to obtain fully working stereo. If a DP-DVI dual link
  adapter is used, the stereo does not work on the top and the
  bottom part of the screen. This is true for a native DELL
  active adaptor or generic models. The exact reason remains
  unresolved, but the solution is to use a direct DP-DP
  connection. This limits the available choice of displays which
  require 120 Hz for 1080*1980 screen resolution and a DP input.
  We have been choosing a “Nvidia 3D ready” model.
 
There has been a considerate about of exchange
  about this problem on
 
https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
 
The setup comes with a price tag of about 1600 €
  free of taxes.
 
coot, pymol and chimera work straight without
  problems in hardware stereo mode. The experience is absolutely
  great.
 
Best
 
Wim 
-- 
Wim Burmeister
  Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
  Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website