date:20230207

Re: [ccp4bb] [EXT] Re: [ccp4bb] [EXT] Re: [ccp4bb] Regarding the diffraction image

2023-02-07 Thread kavyashreem

Dear Patrick, 

I did use microseeding but for a different ligand. Will try with this as
well. 

Thank you 

REgards 

Kavya 

On 2023-02-07 16:20, Patrick Shaw Stewart wrote:

>> As to why previously in a very similar condition you did get your desired 
>> protein plus (other) ligand
> 
> Kavya, did you use microseeding?  That's the way to get consistent results. 
> 
> Since you're changing the ligand I suggest you go back and run a few random 
> screens (with crushed crystals of your protein with the other ligand) - 
> so-called microseed matrix-screening. 
> 
>> https://doi.org/10.1107/S0907444907007652
> 
> Good luck 
> 
> Patrick 
> 
> On Sat, Feb 4, 2023 at 10:32 PM Mark J. van Raaij  
> wrote: 
> PS it's probably not a salt crystal...TCEP is not a salt, your ligand I 
> presume is also not a salt, a small cleaved peptide neither. As to why 
> previously in a very similar condition you did get your desired protein plus 
> (other) ligand crystal, it just means the molecule (TCEP') crystallises in a 
> similar condition to your protein - I don't think you can conclude much more 
> than that (unless there is some other difference like the TCEP being older 
> this time and more oxidised, for example). 
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas, lab 20B
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain 
> tel. +34 91 585 4616 (internal 432092)
> Section Editor Acta Crystallographica F
> https://journals.iucr.org/f/
> 
> On 4 Feb 2023, at 15:48, kavyashreem  wrote: 
> 
> Dear all,  
> 
> Sorry for the confusion created, I did not mean that a protein would have fit 
> in the small unit cell. My question was - 
> 
> 1. Why are there closely spaced spots arising in salt crystal? 
> 
> 2. If TCEP could crystallize in the condition, I have got a protein (same as 
> this)+ligand (different ligand) complex in very close condition. (ligand size 
> is within 500Da). 
> 
> Thank you 
> 
> Kavya 
> 
> On 2023-02-03 14:35, a.perra...@nki.nl wrote: Hi Kavya, 
> 
> Try https://csb.wfu.edu/tools/vmcalc/vm.html  
> 
> This tells you that a 30kD protein simply does not fit the cell. 
> 
> I am pretty sure you crystallised the ligand, or TCEP actually. 
> 
> Also, if you look at the diffractions pattern, its clear the crystal 
> diffracts beyond 1.0A, diffraction spots are really very very very strong at 
> 2.0A. 
> 
> On 3 Feb 2023, at 09:22, kavyashreem  wrote: 
> 
> Dear all, 
> 
> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
> condition 10%PEG3350, 50mM Zinc acetate. 
> 
> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8.  
> 
> Crystal: Crystal:   
> crystal under UV m 
> 
> <8ef9453e.png>
> 
> When we collected the data at an in-house facility, it looked something like 
> this: 
> 
>  
> 
> The minimum resolution spot is around 9Ang and maximum ~2.2Ang. 
> 
> I have not come across a protein diffraction like this, nor of a salt. When I 
> ran the gel for the incubated protein (protein+ligand), there was no 
> degradation. 
> 
> Although, I was sure there is some problem with this image I tried 
> processing, which could not be, But indexing showed a unit cell  of 11Ang, 
> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not the 
> third. 
> 
> Can anyone please shed some light on this diffraction image? 
> 
> How can it happen?
> 
> Thank you 
> 
> Regards 
> 
> Kavya
> 
> -
> 
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[ccp4bb] Graduate Student Positions in Biochemistry and Microbiology

2023-02-07 Thread Gerd Prehna






Graduate student positions in Biochemistry
The Prehna Lab is looking for enthusiastic MSc or PhD students to 
join the Department of Microbiology at the University of Manitoba, Canada 
(https://home.cc.umanitoba.ca/~prehnag/).
Project:
Our lab studies how bacteria communicate with their hosts, how they 
communicate with each other, and how they communicate with other 
micro-organisms. The supported graduate student positions are aimed at 
understanding the Type VI secretion system (T6SS) at the molecular level. A MSc 
or PhD student will research the role of accessory proteins that modulate the 
function of the T6SS(s) and how membrane proteins are loaded and secreted by 
the T6SS using structural and biochemical techniques including x-ray 
crystallography, NMR spectroscopy, and cryo-EM. 
Qualifications:
Applicants should possess or be near completion of a BSc degree in 
Biochemistry or a closely related discipline, and be interested in both 
biochemistry and microbiology. Some experience in molecular biology as well as 
protein expression and purification is desired but not required. English 
language skills, the ability to work in a team, willingness to learn, and good 
organizational skills are required.
Application:
Applications should include:  1. The applicant's CV 2. 
A one-page summary of their motivation for pursing graduate studies 3. 
Contact details for at least two references
The starting dates are May 2023 or September 2023
Please send application materials to: gerd.pre...@umanitoba.ca
Gerd Prehna, PhD Assistant Professor
We invite applications from all qualified individuals. The 
University of Manitoba is strongly committed to equity and diversity within its 
community and welcomes applications from women, racialized persons, Indigenous 
peoples, persons with disabilities, persons of all sexual orientations, persons 
of any gender identity or gender expression, and others who may contribute to 
the further diversification of ideas.
About the University of Manitoba:
The University of Manitoba (http://umanitoba.ca/;>http://umanitoba.ca/) is located in Winnipeg, Manitoba and is 
Western Canada’s first University. The University has large core-group of 
structural biology and biochemical researchers between the departments of 
Microbiology (http://www.sci.umanitoba.ca/microbiology/;>http://www.sci.umanitoba.ca/microbiology/) and Chemistry (The Manitoba 
Group in Protein Structure and Function), access to the Canadian Light Source 
synchrotron, and comprehensive molecular biophysics instrumentation (500 and 
600 MHz NMR, in-house XRD, cryo-3D TEM (TalosF200C), ITC, CD, DSC, nanoDSF, 
AUC, SEC-MALS, and MST).





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[ccp4bb] Postdoc opportunity at the University of South Alabama

2023-02-07 Thread Christopher Davies

Applications from highly qualified candidates are invited for a postdoctoral
position in my lab at the University of South Alabama in Mobile, AL. The
primary focus will be an NIH-funded project investigating PlzA, a
cyclic-di-GMP binding protein from the Lyme disease spirochete, Borreliella
burgdorferi, but there will also be opportunity to contribute to other
projects.

The work will entail site-directed mutagenesis, cloning, purification and
crystallization of proteins, collecting diffraction data, solving structures
by X-ray crystallography, enzyme kinetics and various biophysical techniques
(ITC, fluorescence spectroscopy).

Candidates should hold a PhD in biochemistry or chemistry, with a strong
background in molecular biology, protein crystallography, and preferably
enzyme kinetics. An interest in microbiology and antibiotic resistance is
desirable. Successful candidates will be highly motivated to succeed, able
to think critically, and can work both independently and collaboratively.
Good verbal and written communication skills are essential. 

The University of South Alabama is a comprehensive research and teaching
university located in Mobile, Alabama. Its College of Medicine has 270
faculty members across 17 academic departments, with outstanding cores and
facilities for research, including a BSL-3 facility for infectious disease
research. Construction of a new, state-of-the-art Medical School will
commence later this year. 

Please send cover letter and CV directly to me by email to
 cdav...@southalabama.edu.

Informal enquiries by email are welcome.

 

Christopher Davies, Ph.D.

Professor, Dept. of Biochemistry & Molecular Biology

5795 USA Drive N, CSAB 234

University of South Alabama

Mobile AL 36688

Tel: (251) 341 3826

 




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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2023

2023-02-07 Thread Manfred S. Weiss


Dear all,

the next MX-proposal application deadline: March 01, 2023 is approaching

NEW: REMOTE OPERATION IS NOW THE PREFERRED MODE AT BLs14.1 AND 14.2.
PARTICPATION IN REMOTE TRAINING COURSE IS REQUIRED.

As usual, all proposals will be handled by our electronic user portal GATE,
https://www.helmholtz-berlin.de/pubbin/hzbgate

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(07/2023-12/2023).

In order to apply for beamtime, please register in GATE and submit
a new beam time application proposal.

Please note that we now expect from each research group only ONE proposal,
which can contain up to 20 individual projects.

IMPORTANT: If you have a running 2021-2 or a running 2022-2 proposal, you
may ask for extension. For a 2022-2 proposal, an interim report is necessary,
and for a 2021-2 proposal a full report including highlights. After submitting
the reports to GATE, you will be able to edit and modify your proposals by
adding and deleting projects.

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations in
Germany with more than 4000 PDB depositions in total. Beamtime is granted
based on the reviewed proposals and on reports from previous research
activities. Please make sure to include them if available.

Experimental setup:

BL14.1:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position
 (0.04-1 sec exposure time per frame)
- PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. 
distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer
- Automatic sample changer (CATS), 9 Unipucks, i.e. 144 sample storage capacity
- User defined beam shaping from 50 µm-100 µm diameter possible
- Multi-core XEON-CPU server, with 10GB uplink to Pilatus 6M
- Data collection control via MXCuBE2
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP3
- Remotely controlled cryo-shutter for crystal annealing
- AMPTEK-XRF detector and XFEPLOT software available

BL14.2:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.6x10¹¹ Phot/sec x 100 mA at sample position
 (0.05-1 sec exposure time per frame)
- PILATUS3 S 2M detector with 1000 µm Si sensor thickness,
 85 mm - 800 mm distance from the sample (a special mode with
 56 mm distance is also available upon request for ultra-high
 resolution studies)
- Nanodiffractometer with fast air-bearing axis and on-axis sample
 microscope
- User defined beam shaping from 30 µm-150 µm diameter possible
- Data collection control via MXCuBE2
- ISARA2 sample changer for Unipuck support, Dewar with 29 Unipuck slots
- Multi-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- AMPTEK-XRF detector and XFEPLOT software available
- UV-Microsprectrophotometer offline setup available

If you need atomic resolution or better, BL14.2 is the beamline
of choice for you!!

BL14.3:
- Fixed photon energy: 13.8 keV (wavelength: 0.89 A)
- Photon flux: 1.6x10exp10 Phot/sec x 100mA at sample position
 (3-20 sec exposure time per frame)
- PILATUS 6M detector, 54 mm-450 mm distance from the sample
- MD2S microdiffractometer with mini-kappa goniometer
- RT data collection
- Data collection at 50 K using a He cryostat
- Multi-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Data collection control via MXCuBE2
- Common MX software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- REX rapid nozzle exchanger
- HC-Lab dehydration device installed (please specify HC-Lab-beamtime
 in your proposal if needed)
- AMPTEK-XRF detector and XFEPLOT software available

Other facilities:
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpix CCD-camera
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)

S1-biolab facilities (separate registration required):
- Protein production and purification (AEKTA)
- nL 96-well crystallization plate formulation and storage at
 5°C and 20°C
- Biophysical characterization with real time PCR (thermofluor assay)
- Contactless compound pipetting using ATS

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please see
https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/fragment-screening/index_en.html
or contact

[ccp4bb] postdoc fellowships at Umeå University, Sweden

2023-02-07 Thread Lars-Anders Carlson

Dear all,
There are multiple postdoc fellowships available at Umeå University, within the
collaborative "Excellence by Choice" programme. The projects are within the
general fields of infection and plant biology (two strong research environments
in Umeå). Many have a structural biology component.

The EC fellowships are constructed to encourage early independence, and come
with both a consumables budget and funding for networking/travelling.

One project is a collaboration between myself and organic chemist Christian
Hedberg. We are looking for someone who would like to combine methods from
biochemistry, bio-organic chemistry and cryo-EM to uncover mechanisms of novel
anti-parasitic compounds. People with experience in protein purification are
especially welcome to apply, but we welcome applications from all different
backgrounds.

Have a look at all the projects here:
https://www.umu.se/en/ucmr/ec-postdoc-programme/excellence-by-choice-postdoctoral-programme-in-life-science/

Reach out if you have any questions! Deadline is 19 March.

Best wishes,
Lars

--
Lars-Anders Carlson
Assoc Prof, Dept of Medical Biochemistry and Biophysics
Wallenberg Centre for Molecular Medicine
Molecular Infection Medicine Sweden
Umeå University
90187 Umeå, Sweden
carlsonlab.se

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[ccp4bb] wwPDB news: Prototype of PDB NextGen Archive now available

2023-02-07 Thread Deborah Harrus


Dear all,

A prototype of a next generation archive repository for the PDB is now 
available. The archive, called “NextGen”, hosts structural model files 
in PDBx/mmCIF and PDBML formats atfiles-nextgen.wwpdb.org 
. This enriched PDB archive provides 
annotation from external database resources in the metadata in addition 
to the content provided in the structure model files in the PDB main 
archive atfiles.wwpdb.org .


This prototype provides sequence annotation from external resources such 
as UniProt, SCOP2 and Pfam at atom, residue, and chain levels. This 
mapping information is derived from the Structure Integration with 
Function, Taxonomy and Sequence (SIFTS) project 
(https://www.ebi.ac.uk/pdbe/docs/sifts/), a service developed and 
maintained by the PDBe and UniProt teams at EMBL-EBI. Sequence mappings 
are provided in _pdbx_sifts_unp_segments and 
_pdbx_sifts_xref_db_segments categories for each segment, 
_pdbx_sifts_xref_db at residue level, and _atom_site at atom level.


The PDB NextGen Repository is currently updated monthly on the first 
Wednesday of the month at 00:00 UTC and is subject to change in the 
future. You can access these NextGen files at the following locations:


 * wwPDB:https://files-nextgen.wwpdb.org, rsync://rsync-nextgen.wwpdb.org
 * RCSB PDB (USA):https://files-nextgen.rcsb.org,
   rsync://rsync-nextgen.rcsb.org
 * PDBe (UK):https://ftp.ebi.ac.uk/pub/databases/pdb_nextgen/
 * PDBj (Japan):https://ftp-nextgen.pdbj.org
   

Data are structured based on entry ID with a two letter hash code, 
‘third from last character' and 'second from last character’. This hash 
code will remain consistent once PDB ID codes are extended beyond four 
characters with the pdb_ prefix.


Some examples are shown below:

 * Access entry pdb_8aly
   
athttps://files-nextgen.wwpdb.org/pdb_nextgen/data/entries/divided/al/pdb_8aly/
 * Both PDBx/mmCIF and PDBML are provided at this location. For entry
   pdb_8aly:
 o pdb_8aly_xyz-enrich.cif.gz
 o pdb_8aly_xyz-no-atom-enrich.xml.gz

Please contactinfo@wwpdb.orgwith any questions.

Read this news on the wwPDB website: 
https://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826


Kind regards,

Deborah Harrus

PDBe

--
---
Deborah Harrus, Ph.D.
Lead Annotator
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
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Re: [ccp4bb] [EXT] Re: [ccp4bb] Regarding the diffraction image

2023-02-07 Thread Patrick Shaw Stewart

>
> As to why previously in a very similar condition you did get your desired
> protein plus (other) ligand


Kavya, did you use microseeding?  That's the way to get consistent results.

Since you're changing the ligand I suggest you go back and run a few random
screens (with crushed crystals of your protein with the other ligand) -
so-called microseed matrix-screening.

https://doi.org/10.1107/S0907444907007652


Good luck

Patrick






On Sat, Feb 4, 2023 at 10:32 PM Mark J. van Raaij 
wrote:

> PS it’s probably not a salt crystal…TCEP is not a salt, your ligand I
> presume is also not a salt, a small cleaved peptide neither. As to why
> previously in a very similar condition you did get your desired protein
> plus (other) ligand crystal, it just means the molecule (TCEP')
> crystallises in a similar condition to your protein - I don’t think you can
> conclude much more than that (unless there is some other difference like
> the TCEP being older this time and more oxidised, for example).
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas, lab 20B
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. +34 91 585 4616 (internal 432092)
> Section Editor Acta Crystallographica F
> https://journals.iucr.org/f/
>
>
> On 4 Feb 2023, at 15:48, kavyashreem  wrote:
>
> Dear all,
>
> Sorry for the confusion created, I did not mean that a protein would have
> fit in the small unit cell. My question was -
>
> 1. Why are there closely spaced spots arising in salt crystal?
>
> 2. If TCEP could crystallize in the condition, I have got a protein (same
> as this)+ligand (different ligand) complex in very close condition. (ligand
> size is within 500Da).
>
> Thank you
>
> Kavya
>
>
> On 2023-02-03 14:35, a.perra...@nki.nl wrote:
>
> Hi Kavya,
>
> Try https://csb.wfu.edu/tools/vmcalc/vm.html
>
> This tells you that a 30kD protein simply does not fit the cell.
>
> I am pretty sure you crystallised the ligand, or TCEP actually.
>
> Also, if you look at the diffractions pattern, its clear the crystal
> diffracts beyond 1.0A, diffraction spots are really very very very strong
> at 2.0A.
>
>
>
> On 3 Feb 2023, at 09:22, kavyashreem  wrote:
>
> Dear all,
>
> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the
> condition 10%PEG3350, 50mM Zinc acetate.
>
> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH
> 8.
>
> Crystal: Crystal:
> crystal under UV m
>
> <8ef9453e.png>
>
> When we collected the data at an in-house facility, it looked something
> like this:
>
> 
>
> The minimum resolution spot is around 9Ang and maximum ~2.2Ang.
>
> I have not come across a protein diffraction like this, nor of a salt.
> When I ran the gel for the incubated protein (protein+ligand), there was no
> degradation.
>
> Although, I was sure there is some problem with this image I tried
> processing, which could not be, But indexing showed a unit cell  of 11Ang,
> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not
> the third.
>
> Can anyone please shed some light on this diffraction image?
>
> How can it happen?
>
>
> Thank you
>
> Regards
>
> Kavya
>
>
> --
>
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-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36



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[ccp4bb] Doctoral position in Munich, Germany

2023-02-07 Thread Ana Messias

Dear All,

A doctoral student position is available to work with Dr. Ana Messias and Prof.
Michael Sattler , at the Institute
of Structural Biology (Helmholtz Munich, HMGU) and the Bavarian NMR Center at
the TUM School of Natural
Sciences in Munich, Germany . The successful applicant will be joining a
dynamic, interdisciplinary and international
lab, within one of the world’s top research institutes and universities. We are
seeking a highly motivated and enthusiastic
candidate with a background in structural biology/biochemistry/biophysics and a
strong interest in molecular mechanisms
of human disease.
This exciting doctoral project will investigate the detailed molecular and
functional mechanism of the enigmatic protein
C19orf12 and its role in the development of Mitochondrial-membrane
Protein-Associated Neurodegeneration (MPAN) .

For more details please check the website:
https://www.findaphd.com/phds/project/structural-and-functional-investigation-of-the-protein-c19orf12-involved-in-the-neurodegenerative-disease-mpan/?p155066

Best regards,
Ana Messias

Dr. Ana Messias
Team Leader Metabolic and Neurodegenerative Diseases
Helmholtz Munich
Institute of Structural Biology
Building 43b Room 103
Ingolstädter Landstraße 1
85764 Neuherberg
Germany

Tel: +49 89 3187 4706
Fax: +49 89 3187 174706
Email: [ mailto:ana.mess...@helmholtz-munich.de |
ana.mess...@helmholtz-munich.de ]

[ http://www.helmholtz-munich.de/ | www.helmholtz-munich.de ]

Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und
Umwelt (GmbH), Ingolstadter Landstr. 1, 85764 Neuherberg,
www.helmholtz-munich.de. Geschaeftsfuehrung: Prof. Dr. med. Dr. h.c. Matthias
Tschoep, Kerstin Guenther, Daniela Sommer (kom.) | Aufsichtsratsvorsitzende:
Prof. Dr. Veronika von Messling | Registergericht: Amtsgericht Muenchen HRB
6466 | USt-IdNr. DE 129521671