[ccp4bb] CBMS Lecture Series - Andrea Dessen - March 20

2024-03-15 Thread Stojanoff, Vivian 
You are cordially invited to join  the Center for Biomolecular Structure 
Lecture Series ………..





Andrea Dessen


CNRS Research Director


Institut de Biologie Structurale, France





WEDNESDAY, March 20, 13:30 (EDT)



"Architecture and Genomic Arrangement of Bacterial Cell Biosynthesis Complexes"



Register in advance for this meeting:


https://bnl.zoomgov.com/meeting/register/vJIsdOysqzoiHJzcKLSKZqX5jfwZQcIozkM



   Time conversion Link: 
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Abstract: The bacterial cell wall is important for survival and shape, and its 
biosynthetic mechanism is the target of beta-lactam antibiotics. The spread of 
resistant strains, however, has limited the usefulness of these drugs and calls 
for efforts towards studies of cell wall formation that could lead to the 
development of innovative treatments. My group is interested in structurally 
and functionally characterizing protein complexes involved in both cytoplasmic 
and periplasmic steps of cell wall biosynthesis. The synthesis of 
peptidoglycan, the main component of the cell wall, starts in the cytoplasm, 
through sequential reactions catalyzed by Mur enzymes that have been suggested 
to associate into a multi-membered complex. This idea is supported by the 
observation that in many bacteria, mur genes are present in a single operon 
within the well conserved dcw cluster, and in some cases pairs of mur genes are 
fused to encode a single, chimeric polypeptide able to catalyze successive 
reactions. I will present the crystal structure of the MurE-MurF chimera from 
Bordetella pertussis, which reveals a head-to-tail, elongated architecture and 
indicates how sequential reactions could be catalyzed. In addition, I will also 
discuss structural details of complexes formed in the bacterial periplasm, 
notably between Penicillin-Binding Proteins (PBPs) and the scaffolding protein 
MreC, that act in partnership with Mur proteins in the cell wall biosynthesis 
process. These structural and functional insights shed light on the importance 
of studying pathways that are of critical relevance for bacterial cell survival 
in light of the antibiotic resistance crisis..



==



Vivian Stojanoff, PhD

Education, Training, Outreach

User Program

p 1(631) 344 8375

e lifescie...@bnl.gov

w https://www.bnl.gov/ps/lifesciences/



Address:

Center for Biomolecular Structure

National Synchrotron Light Source II

Building 745

Brookhaven National Laboratory

Upton NY 11973





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[ccp4bb] Postdoctoral Fellow position in Membrane Protein Biochemistry and Cryo-EM

2024-03-15 Thread Ankita Punetha 
Dear Colleagues,

A postdoctoral fellow position is available in the Petrou lab at Rutgers
New Jersey Medical School (NJMS) to support NIH-funded research. Our
research focuses on the structural biology of membrane (and soluble)
proteins using single particle cryo-electron microscopy (cryo-EM).



The Postdoctoral Fellow will be responsible for the expression and
purification of proteins using bacterial, insect and mammalian heterologous
expression systems, and for the structure determination of membrane
proteins and/or protein complexes by single-particle cryo-EM. In addition,
the Postdoctoral Fellow will be responsible for biophysical and biochemical
characterization of target proteins, including protein-ligand or
protein-protein interactions.



Candidates must have a Ph.D. in Structural Biology, Molecular Biology,
Biochemistry, or related fields. Experience with heterologous expression of
proteins using insect cell or mammalian cell systems is necessary for this
position. Additionally, preference will be given to candidates with
experience in structure determination of proteins by single-particle
cryo-EM and atomic model building/validation. Good communication &
organizational skills and the ability to work independently are important
for this position. Salary will be commensurate to the candidate’s
experience and qualifications and based on the Rutgers postdoc salary scale.



The Petrou Lab is located in Newark, New Jersey, 20 min away from New York
city. The Rutgers NJMS Cryo-EM Core facility (RNCCF), located in the same
building as the Petrou Lab, provides access to a 100kV Tundra microscope
with speed-enhanced Ceta camera, and sample preparation equipment.
Additionally, the Rutgers Cryo-EM and Nanoimaging facility (RCNF), located
in Piscataway, New Jersey, provides access to further cryo-EM and cryo-ET
instrumentation, including a 200kV Talos Arctica microscope, an Aquilos 2
FIB-SEM microscope, and a Leica cryo-CLEM setup. A 300kV Krios microscope
equipped with K3 direct detector and energy filter is expected to be
installed later this year at RNCF.



Interested candidates can find additional information and apply online at:
https://jobs.rutgers.edu/postings/220441



A short cover letter, a CV and contact information for three references are
required. Candidates will be evaluated on a rolling basis until the
position is filled.



For further information, candidates can contact Dr. Petrou via email (
vasileios.pet...@rutgers.edu) or direct message on Twitter
(@VasileiosPetrou) or LinkedIn.




Best,

Ankita


*Ankita Punetha, Ph.D. (She/Her)*

*Research Associate II, Petrou Lab*

Rutgers New Jersey Medical School

Department of Microbiology, Biochemistry and Molecular Genetics,

And Center of Immunity and Inflammation (CII)

*Lab:* 973-972-5217 (E430L.2)   *Email:* ankita.pune...@rutgers.edu
*Twitter:* @ankitapunetha 

*Address:* 225 Warren Street, Newark, NJ 07103 (ICPH)



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[ccp4bb] Postdoctoral fellow position is available in the Petrou lab at Rutgers New Jersey Medical School

2024-03-15 Thread Ankita Punetha 
Dear Colleagues,

A postdoctoral fellow position is available in the Petrou lab at Rutgers
New Jersey Medical School (NJMS) to support NIH-funded research. Our
research focuses on the structural biology of membrane (and soluble)
proteins using single particle cryo-electron microscopy (cryo-EM).



The Postdoctoral Fellow will be responsible for the expression and
purification of proteins using bacterial, insect and mammalian heterologous
expression systems, and for the structure determination of membrane
proteins and/or protein complexes by single-particle cryo-EM. In addition,
the Postdoctoral Fellow will be responsible for biophysical and biochemical
characterization of target proteins, including protein-ligand or
protein-protein interactions.



Candidates must have a Ph.D. in Structural Biology, Molecular Biology,
Biochemistry, or related fields. Experience with heterologous expression of
proteins using insect cell or mammalian cell systems is necessary for this
position. Additionally, preference will be given to candidates with
experience in structure determination of proteins by single-particle
cryo-EM and atomic model building/validation. Good communication &
organizational skills and the ability to work independently are important
for this position. Salary will be commensurate to the candidate’s
experience and qualifications and based on the Rutgers postdoc salary
scale.



The Petrou Lab is located in Newark, New Jersey, 20 min away from New York
city. The Rutgers NJMS Cryo-EM Core facility (RNCCF), located in the same
building as the Petrou Lab, provides access to a 100kV Tundra microscope
with speed-enhanced Ceta camera, and sample preparation equipment.
Additionally, the Rutgers Cryo-EM and Nanoimaging facility (RCNF), located
in Piscataway, New Jersey, provides access to further cryo-EM and cryo-ET
instrumentation, including a 200kV Talos Arctica microscope, an Aquilos 2
FIB-SEM microscope, and a Leica cryo-CLEM setup. A 300kV Krios microscope
equipped with K3 direct detector and energy filter is expected to be
installed later this year at RNCF.



Interested candidates can find additional information and apply online at:
https://jobs.rutgers.edu/postings/220441



A short cover letter, a CV and contact information for three references are
required. Candidates will be evaluated on a rolling basis until the
position is filled.



For further information, candidates can contact Dr. Petrou via email (
vasileios.pet...@rutgers.edu) or direct message on Twitter
(@VasileiosPetrou) or LinkedIn.




Best wishes,

Ankita


*Ankita Punetha, Ph.D. (She/Her)*

*Research Associate II, Petrou Lab *

Rutgers New Jersey Medical School

Department of Microbiology, Biochemistry and Molecular Genetics,

And Center of Immunity and Inflammation (CII)

*Lab:* 973-972-5217 (E430L.2)   *Email:* ankita.pune...@rutgers.edu
*Twitter:* @ankitapunetha 

*Address:* 225 Warren Street, Newark, NJ 07103 (ICPH)



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Re: [ccp4bb] isymop reference for ISYM column in MTZ files

2024-03-15 Thread Robbie Joosten 
If I understand the documentation correctly (https://www.ccp4.ac.uk/html/mtzformat.html), it refers to the symmetry operations as they are stored in the header of the MTZ file. So the source of the MTZ file might make a difference. The safest way of using this data is to follow the header and not some implied order.HTH,RobbieOn 15 Mar 2024 04:59, "Hekstra, Doeke Romke"  wrote:

Hi, 
 
I would like to be sure about which symmetry operation the M/ISYM column in an MTZ file is referring to. Is it correct that this matches the order in CCP4’s /lib/data/syminfo.lib (at least when this order is unique—it is not always so)?
 Would anyone know why the order in one of my favorite websites (http://img.chem.ucl.ac.uk/sgp/large/sgp.htm) happens to often be different?
 
Thank you,
Doeke
 
=  
 
Doeke Hekstra
Assistant Professor of Molecular & Cellular Biology, and of Applied Physics (SEAS),
Director of Undergraduate Studies, Chemical and Physical Biology
Center for Systems Biology, Harvard University
52 Oxford Street, NW311
Cambridge, MA 02138
Office:    617-496-4740
Admin:   617-495-5651 (Lin Song)
 
 




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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-15 Thread Rangana Warshamanage 
The line causing troubles is SFAC, I think


On Thu, 14 Mar 2024, 22:44 Navdeep Sidhu,  wrote:

> Dear Fred,
>
> I hope you'd agree that another good way to bypass similar issues is
> that before working on data where you don't know the model, you try out
> data where you do. And so I'd recommend this book, which provides you
> with practice data and great worked tutorials:
>
> Peter Müller (Ed.). Crystal Structure Refinement: A Crystallographer's
> Guide to SHELXL.  IUCr/Oxford, 2006
> .
>
> The book uses XP for visualization (which I guess some people still use)
> but, as Tim suggested, you should certainly also try out ShelXle or
> Olex2. (I think it's fair to say that we couldn't have identified some
> density issues just using XP.)
>
> (A 2nd edition of the book would also be a great idea.)
>
> Best regards,
> Navdeep
>
> ---
> Navdeep Sidhu
> Germany
> Web: https://scholar.google.de/citations?user=ZqU1AE0J=de
> ---
>
>
> ---
> On 12.03.24 16:42, Frederic Vellieux wrote:
> > Hi,
> >
> > In fact the problem was solved with the help of Ivica Dilovic from
> > Zagreb who suggested some changes to the shelxl .ins file. After these
> > modifications the cryptic error message was still there, but the
> > modifications made me try to remove one card. That did it.
> >
> > So the part that is concerned with this error in the .ins file is as
> > follows:
> >
> > did not work and gave the cryptic error message:
> > TITL 240223Ru_complex_0m_5 in P1
> > CELL 1.34139  10.36240  11.17780  13.19300  80.8589  73.7519  71.3166
> > ZERR2.00   0.00070   0.00080   0.00090   0.0026   0.0023   0.0023
> > LATT -1
> > SFAC C H N O CL RU
> > UNIT 62 64 2 10 2 2
> > TEMP -163.150
> > TREF
> > L.S. 10
> > EXTI 0.001
> > WGHT 0.0617
> > BOND $H
> > CONF
> > HTAB
> > FMAP 2
> > PLAN 20
> > FVAR 0.75351
> >
> > worked and gave no error:
> > TITL 240223Ru_complex_0m_5 in P1
> > CELL 1.34139 10.3624 11.1778 13.193 80.8589 73.7519 71.3166
> > ZERR 2 0.0007 0.0008 0.0009 0.0026 0.0023 0.0023
> > LATT -1
> > SFAC C H N O Cl Ru
> > DISP C 0.0137 0.0067 57.1
> > DISP Cl 0.3281 0.5435 4162.2
> > DISP H 0 0 0.6
> > DISP N 0.0241 0.0134 109.9
> > DISP O 0.0389 0.0241 193.4
> > DISP Ru -0.076 2.5955 20068.6
> > UNIT 62 64 2 10 2 2
> > L.S. 10
> > PLAN  10
> > TEMP -163.15
> > CONF
> > BOND $H
> > HTAB
> > MORE -1
> > fmap 2
> > WGHT 0.1
> > FVAR 0.25491
> >
> > I guess it would be much better (from the user's point of view) if
> > SHELXL would write on the output what the offending line is.
> >
> > Also, no indications are given on the SHELX site where the Windows .exe
> > files are supposed to go. They must be placed in the directory where the
> > GUI (olex2 or WingX) stores its exe file (olex2.exe or wingx.exe). I
> > just tried to place them there because I was desperate and it worked.
> >
> > Cheers, and thanks to everyone for their suggestions.
> >
> > Fred.
> >
> > On 2024-03-12 16:12, Kay Diederichs wrote:
> >> Fred,
> >>
> >> nobody would be offended if you'd just post your SHELXL .ins file
> >> here; there are enough experienced crystallographers to spot the
> mistake.
> >> Best would be if you could pare it down to small size, but such that
> >> it is still reproducible (my own experience is that this almost always
> >> makes me find my own mistakes).
> >>
> >> But to try and answer your title question, there is the
> >> bruker-...@g-groups.wisc.edu mailing list.
> >>
> >> Best wishes,
> >> Kay
> >>
> >> 
> >>
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> > 
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