[ccp4bb] Scientists positions open in Structural Genomics

[Karla J. F. Satchell]

The Northwestern Feinberg School of Medicine is seeking a Protein Purification 
and Crystallization Expert with an open rank for PostDoc, Research Associate, 
or Senior Research Associate to participate in a Structural Genomics Research 
Center addressing important biochemical studies related to infectious diseases. 
Protein targets are predominantly bacterial with some viral studies in topics 
of pathogenesis, antimicrobial resistance, and drug discovery. The center has 
just been renewed for funding through 2027.
https://www.feinberg.northwestern.edu/sites/csgid 

https://www.feinberg.northwestern.edu/faculty-profiles/az/profile.html?xid=10285
 



Apply online at
LinkedIn : https://www.linkedin.com/jobs/view/2780013014/ 


>  Or Indeed: 
> https://www.indeed.com/viewjob?t=protein+purification+and+crystallization+expert=4c34dc6912411c96&_ga=2.46279267.594172634.1661434147-1829229600.1661434147
>  
> 

Person must have expertise in protein crystallization, preferably including 
complexes and/or soaking with ligands. Person will be responsible to carry 
projects from design of plasmids for commercial synthesis, protein expression 
and purification to protein crystallization, crystal monitoring and freezing. 
Crystallography experience is helpful although this person will work closely 
with experienced crystallographers and thus crystallographic data collection 
and analysis is not essential.

Communication skills are important as person will work directly with persons 
from outside labs to pursue studies. Ability to work with other team members to 
create a positive working environment is essential.

Position is open immediately and will remain open until filled. The position 
could be suitable for person who require a Visa to work in the US.

It is expected that candidates will either hold a Ph.D. or have a minimum of 
six years relevant experience in protein purification and crystallization. More 
experienced candidates encouraged to apply. Salary will be set competitive with 
experience level.

Northwestern University is an Equal Opportunity, Affirmative Action Employer of 
all protected classes, including veterans and individuals with disabilities. 
Women, racial and ethnic minorities, individuals with disabilities, and 
veterans are encouraged to apply. Hiring is contingent upon eligibility to work 
in the United States.

Job Type: Full-time

Pay:Salary will be set based on level of experience

Benefits:

401(k) matching
Dental insurance
Flexible spending account
Health insurance
Health savings account
Life insurance
Paid time off
Retirement plan
Tuition reimbursement
Vision insurance
Schedule:

Monday to Friday
Weekend availability
COVID-19 considerations:

Currently NU requires vaccination and has free testing options available. Masks 
are optional. Please review the up-to-date policies at 
https://www.northwestern.edu/coronavirus-covid-19-updates/information-for/staff/index.html
 
.
 


Karla J. F. Satchell, Ph.D.
Anne Stewart Youmans Professor of Microbiology,
Northwestern University Feinberg School of Medicine
PI & Co-Director, Center for Structural Genomics of Infectious Diseases
Dept. of Microbiology-Immunology
303 E. Chicago Avenue, Ward 6-205
Chicago, IL 60611
312-503-2162
k-satch...@northwestern.edu 








Karla J. F. Satchell, Ph.D.
Anne Stewart Youmans Professor of Microbiology,
Northwestern University Feinberg School of Medicine
PI & Co-Director, Center for Structural Genomics of Infectious Diseases
Dept. of Microbiology-Immunology
303 E. Chicago Avenue, Ward 6-205
Chicago, IL 60611
312-503-2162
k-satch...@northwestern.edu








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Re: [ccp4bb] Refmac5 occupancy group by residue name

[James Holton]

Maybe this will help?
https://bl831.als.lbl.gov/~jamesh/scripts/refmac_occupancy_setup.com

Make a pdb file of the residues you want to occupancy-refine and put it 
on the command line of this script, along with the word "allatoms".


This will generate a file called "refmac_opts_occ.txt" that you can 
import into your refmac run.  Possibly using the "@" keyword?


HTH

-James Holton
MAD Scientist


On 9/13/2022 6:59 AM, Evgenii Osipov wrote:

Dear CCP4 community,

  I am refining several structures of multimeric protein-ligand complexes and I 
wanted to refine occupancy of the ligand. Manual definition of groups would be 
tedious and error prone considering that ASU contains 10 protein chains and 1-8 
bound ligand molecules. Hence my idea was to define occupancy group for ligands 
using residue name, e.g. LIG.

According to manual page 
(http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html) I could specify 
occupancy refinement group using chain, residue intervals, atom names and alt 
code. However, residue names are not mentioned inside “Occupancy refinement” 
paragraph.

Is it possible to define occupancy groups in refmac5 using residue name?


Kind regards,





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Re: [ccp4bb] suggestions on refinement of a protein-ligand complex

[Eleanor Dodson]

We probably need more detail to help you.
Have you looked carefully at the data processing? Is the Rmerge or Rpim
reasonable for all batches?   Is there any suggestion of twinning? Does the
wilson plot look linear? (These hexagonal SGs can be twinned)

How many copies of your molecule do you expect?  Then the model you have
used.. What is the sequence ID to the protein, and do you have a suitable
model for the ligand?
I would run a search in all possible SGS - and do the results clearly
indicate one choice is better than all others>

The final check is in the refinement - does the R value fall (FreeR should
too, but your resolution is rather low

Now you run the molecular replacement in all possible spacegroups for  that
pointgroup.. Is there a clear indication of one being preferred?
Good luck. Eleanor


On Tue, 13 Sept 2022 at 18:29, Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Dear Deepak,
>
> I guess that the spacegroup in the MTZ file that you use for refinement is
> wrong.
>
> I think you should carefully check the output of PHASER, and in particular
> the PDB file that it wrote. The correct spacegroup is given there (and it
> may also be P4122  or P4222 or P4322, because likely you used the PHASER
> option that tests all possibilities), and you will have to create a MTZ
> file for refinement that has that particular spacegroup in its header.
>
> Hope this helps, & best wishes
> Kay
>
> On Tue, 13 Sep 2022 11:20:44 +0200, Deepak Deepak 
> wrote:
>
> >Dear all,
> >
> >Greetings from Munich. I hope everything is well with you. I am writing to
> >take input on a problem related to the structure solution of a
> >protein-ligand complex.
> >
> >I have crystallized a protein (7.6kDa) with a ligand (5.2kDa). The crystal
> >diffracted to *2.71 Angstron*, and the data were processed using XDS.
> >During the XDS processing, Pointless suggested data be either P6222 (180
> >space group) or P6422 (181 space group) with a 98% probability.
> >The data were processed as *P6422*.
> >
> >Afterward, I ran Phaser MR with protein's PDB as a search ensemble, and I
> >found a good solution (with a good TFZ score) for protein alone, where I
> >could see some weak density for my ligand.
> >In the next step, I ran Phaser MR with a *modeled PDB* of the Ligand as
> >search ensemble + *using the partial solution from the previous Phaser MR
> >run of Protein*. This Phaser MR run gave me a good fit of ligand onto
> >protein surface with nice density for both molecules.
> >
> >Next, I went ahead with the refinement of this complex. The R-free, in the
> >beginning, was 0.55. In the first round of refinement, it went down to
> >*0.53,* but in the subsequent rounds, it even* increased*. I am stuck at
> >this point and unsure how to proceed. I tried different strategies to
> >refine it, but nothing worked.
> >Could the space group have been wrong? How can I make sure that? I can
> >provide a more detailed explanation to help you better understand the
> >problem.
> >I appreciate your suggestions and input on this matter.
> >
> >Kind regards,
> >Deepak,
> >Ph.D. student,
> >LMU Munich, Germany.
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
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> >
>
> 
>
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[ccp4bb] Postdoctoral positions at the Institute for Structural Biology, Grenoble

[Malene Ringkjobing Jensen]

Two postdoctoral positions are available in the team of Dr. Malene R. Jensen at 
the Institute for Structural Biology in Grenoble, France. 

The successful candidates will study the assembly of scaffolding complexes in 
the mitogen-activated protein kinase (MAPK) cell signalling pathways. In 
particular, the candidates will characterise the structure, dynamics and 
interactions of intrinsically disordered scaffold proteins and elucidate how 
liquid-liquid phase separation contributes to MAPK enzymatic activity. The 
group uses NMR spectroscopy and X-ray crystallography in combination with 
biophysical techniques. The positions are available from the 1st of January 
2023, initially for 2 years with a possible extension of up to 4 years.  

More information can be found on the team website: www.jensen-nmr.fr 


Facilities
The Institute for Structural Biology  is 
located on the EPN science campus in Grenoble in close proximity to the 
European Synchrotron Radiation Facility (ESRF), the European Molecular Biology 
Laboratory (EMBL) Grenoble Outstation and the Institute Laue-Langevin (ILL). 
The IBS houses six high-field NMR spectrometers (3 x 600, 700, 850 and 950 MHz) 
and wetlab facilities for cloning, expression and purification of proteins. 
Access is facilitated to a number of state-of-the-art research platforms 
through Integrated Structural Biology Grenoble .

Qualifications
The ideal candidate holds a PhD in chemistry, biochemistry or biophysics (or 
related discipline) and has experience in protein expression and purification 
and a proven track-record in solution NMR spectroscopy and/or X-ray 
crystallography. To apply for this position, please send your CV, a motivation 
letter and the names of two references to malene.ringkjobing-jen...@ibs.fr 


Recent relevant publications

L. Mariño Pérez, F.S. Ielasi, L.M. Bessa, D. Maurin, J. Kragelj, M. Blackledge, 
N. Salvi, G. Bouvignies, A. Palencia, M.R. Jensen
Nature (2022), 602, 695-700. 

Visualizing protein breathing motions associated with aromatic ring flipping

J. Kragelj, T. Orand, E. Delaforge, L. Tengo, M. Blackledge, A. Palencia, M.R. 
Jensen
Biomolecules (2021),11,1204. 
Enthalpy-entropy compensation in the promiscuous interaction of an 
intrinsically disordered protein with homologous protein partners

K.K. Rasmussen, A. Palencia, A.K. Varming, H. El-Wali, E. Boeri Erba, M. 
Blackledge, K. Hammer, T. Herrmann, M. Kilstrup, L. Lo Leggio, M.R. Jensen
Proc. Natl. Acad. Sci. U.S.A. (2020) 117, 20576-20585. 

Revealing the mechanism of repressor inactivation during switching of a 
temperate bacteriophage

R. Schneider, M. Blackledge, M.R. Jensen 
Curr. Opin. Struct. Biol. (2019) 54, 10-18. 

Elucidating binding mechanisms and dynamics of intrinsically disordered protein 
complexes using NMR spectroscopy

E. Delaforge, J. Kragelj, L. Tengo, A. Palencia, S. Milles, G. Bouvignies, N. 
Salvi, M. Blackledge, M.R. Jensen
J. Am. Chem. Soc. (2018) 140, 1148-1158. 

Deciphering the dynamic interaction profile of an intrinsically disordered 
protein by NMR exchange spectroscopy

J. Kragelj, A. Palencia, M. Nanao, D. Maurin, G. Bouvignies, M. Blackledge, 
M.R. Jensen
Proc. Natl. Acad. Sci. (2015) 112, 3409-3414. 

Structure and dynamics of the MKK7-JNK signalling complex

-- 
Dr. Malene Ringkjøbing Jensen
Research Director CNRS
Institut de Biologie Structurale
71, avenue des Martyrs
CS 10090
38044 Grenoble CEDEX 9
France


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Re: [ccp4bb] suggestions on refinement of a protein-ligand complex

[Kay Diederichs]

Dear Deepak,

I guess that the spacegroup in the MTZ file that you use for refinement is 
wrong.

I think you should carefully check the output of PHASER, and in particular the 
PDB file that it wrote. The correct spacegroup is given there (and it may also 
be P4122  or P4222 or P4322, because likely you used the PHASER option that 
tests all possibilities), and you will have to create a MTZ file for refinement 
that has that particular spacegroup in its header.

Hope this helps, & best wishes
Kay

On Tue, 13 Sep 2022 11:20:44 +0200, Deepak Deepak  
wrote:

>Dear all,
>
>Greetings from Munich. I hope everything is well with you. I am writing to
>take input on a problem related to the structure solution of a
>protein-ligand complex.
>
>I have crystallized a protein (7.6kDa) with a ligand (5.2kDa). The crystal
>diffracted to *2.71 Angstron*, and the data were processed using XDS.
>During the XDS processing, Pointless suggested data be either P6222 (180
>space group) or P6422 (181 space group) with a 98% probability.
>The data were processed as *P6422*.
>
>Afterward, I ran Phaser MR with protein's PDB as a search ensemble, and I
>found a good solution (with a good TFZ score) for protein alone, where I
>could see some weak density for my ligand.
>In the next step, I ran Phaser MR with a *modeled PDB* of the Ligand as
>search ensemble + *using the partial solution from the previous Phaser MR
>run of Protein*. This Phaser MR run gave me a good fit of ligand onto
>protein surface with nice density for both molecules.
>
>Next, I went ahead with the refinement of this complex. The R-free, in the
>beginning, was 0.55. In the first round of refinement, it went down to
>*0.53,* but in the subsequent rounds, it even* increased*. I am stuck at
>this point and unsure how to proceed. I tried different strategies to
>refine it, but nothing worked.
>Could the space group have been wrong? How can I make sure that? I can
>provide a more detailed explanation to help you better understand the
>problem.
>I appreciate your suggestions and input on this matter.
>
>Kind regards,
>Deepak,
>Ph.D. student,
>LMU Munich, Germany.
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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>



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[ccp4bb] Refmac5 occupancy group by residue name

[Evgenii Osipov]

Dear CCP4 community,

 I am refining several structures of multimeric protein-ligand complexes and I 
wanted to refine occupancy of the ligand. Manual definition of groups would be 
tedious and error prone considering that ASU contains 10 protein chains and 1-8 
bound ligand molecules. Hence my idea was to define occupancy group for ligands 
using residue name, e.g. LIG. 

According to manual page 
(http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html) I could specify 
occupancy refinement group using chain, residue intervals, atom names and alt 
code. However, residue names are not mentioned inside “Occupancy refinement” 
paragraph. 

Is it possible to define occupancy groups in refmac5 using residue name?


Kind regards,

-- 

Evgenii Osipov

Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O

mobile: +32 484 38 26 01



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[ccp4bb] ONE WEEK TO APPLY: DLS/CCP4 data analysis workshop 2022

[David Waterman]

Hi folks,

A reminder: there is one week left to apply for this year's DLS/CCP4
workshop. Please see below for details.

Best wishes
-- David


On Tue, 6 Sept 2022 at 13:31, David Waterman  wrote:

> We are pleased to announce that the 9th joint Diamond-CCP4 Workshop on MX
> data collection and structure solution is now open for applications.
> Bringing together leading experts in the field of MX to teach best practice
> in data collection and analysis, this course is aimed at PhD students,
> postdocs and early career scientists who have a focus on structural biology.
>
> After the last two remote events limited to online-only using Zoom, we are
> very happy to report that we intend to go back to an in-person workshop
> this year! However, having learned from the online-only workshops, we will
> keep two remote setup days prior to the on-site element, and we will make
> use of a Slack workspace through the course.
>
> It is essential that applicants commit to attending the workshop in its
> entirety. Please note below the workshop days and timings involved:
>
> - First online preparation day (before fishing crystals): Monday 17 October
> - Second online preparation day (before data collection): Tuesday 22
> November
> - On-site: Monday 28 November to Tuesday 6 December
> - Day off: Saturday 3 December
>
> There is no fee to attend this online workshop, however attendance will be
> subject to an application process and a letter of support from the
> attendee's supervisor will be required. Both the application form and
> supervisor's letter of support will need to be submitted by 17:00 (UK time)
> on 20 September 2022.
>
> Some prior experience of crystallography and data collection is expected,
> and those who already have an interesting project (crystals and possibly
> previously collected datasets) will be given priority in selection.
>
> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2022/
> - Apply at the Diamond website:
> https://www.diamond.ac.uk/Home/Events/2022/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2022.html
>
> -- David (on behalf of the organisers)
>
>



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[ccp4bb] suggestions on refinement of a protein-ligand complex

[Deepak Deepak]

Dear all,

Greetings from Munich. I hope everything is well with you. I am writing to
take input on a problem related to the structure solution of a
protein-ligand complex.

I have crystallized a protein (7.6kDa) with a ligand (5.2kDa). The crystal
diffracted to *2.71 Angstron*, and the data were processed using XDS.
During the XDS processing, Pointless suggested data be either P6222 (180
space group) or P6422 (181 space group) with a 98% probability.
The data were processed as *P6422*.

Afterward, I ran Phaser MR with protein's PDB as a search ensemble, and I
found a good solution (with a good TFZ score) for protein alone, where I
could see some weak density for my ligand.
In the next step, I ran Phaser MR with a *modeled PDB* of the Ligand as
search ensemble + *using the partial solution from the previous Phaser MR
run of Protein*. This Phaser MR run gave me a good fit of ligand onto
protein surface with nice density for both molecules.

Next, I went ahead with the refinement of this complex. The R-free, in the
beginning, was 0.55. In the first round of refinement, it went down to
*0.53,* but in the subsequent rounds, it even* increased*. I am stuck at
this point and unsure how to proceed. I tried different strategies to
refine it, but nothing worked.
Could the space group have been wrong? How can I make sure that? I can
provide a more detailed explanation to help you better understand the
problem.
I appreciate your suggestions and input on this matter.

Kind regards,
Deepak,
Ph.D. student,
LMU Munich, Germany.



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[ccp4bb] superposition & the pairwise CA-distance plots

[이상기]

Dear All,

Please suggest me a program to compute the pairwise CA-distance plots of
residues in other subunits after superposition of one particular subunit.
My enzyme is a homotetrameric one and upon binding of a substrate there are
changes in relative orientations among four subunits (i.e., allosteric
effects). Therefore, I would like to superpose one particular subunit
between an unliganded and a substrate-bound structure, and compute the
pairwise CA-distance plots of equivalent residues in other three subunits.
By using these approaches, I could find out a relative movement of subunits
in a tetramer..

 

Thanks in advance

Sangkee

 

 

==

Sangkee Rhee, Ph.D.

College of Agrculture & Life Sciences

Seoul National University

SEOUL, KOREA

 

e-mail:  srhee...@snu.ac.kr  

==

 




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