- phenixbb - phenix-online.org

(no subject)
by Smita Yadav 30 Jul '21

30 Jul '21

Hello all, Can someone suggest to me, how we can decide the resolution range in the outer shell during the protein crystal data set. And one more thing. processing into different Laue groups and point groups how much it will change the dataset. -- With Regards Smita Yadav

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Visiting Research Specialist Position | Polikanov Lab | University of Illinois at Chicago
by Yury Polikanov 27 Jul '21

27 Jul '21

The Polikanov Lab is seeking a Visiting Research Specialist. The successful candidate will conduct research by using X-ray crystallography techniques to obtain a structural basis for various functions of the bacterial ribosome and its inhibition by different small-molecule inhibitors. The successful candidate should have a strong theoretical background in standard biochemical, molecular biology, and biophysical methods, as well as practical skills in the most standard methods currently used in molecular biology and biochemistry (such as protein expression, purification, etc.). Knowledge in X-ray crystallography or other structural techniques is desired but not required. Expert-level knowledge of the programming languages (such as Python) is highly desirable. The successful candidate would conduct his own research and assist with the principal investigator’s research while training other laboratory personnel in various techniques, experiments, and the appropriate use of research equipment. He/She would also perform data analysis and manage, document, and help with the dissemination of research activities for publication and outreach. *Duties:* • Perform research relevant to the assigned projects; • Isolate and crystallize bacterial ribosomes; • Purify all additional components necessary for the crystallization experiments, such as recombinant proteins, tRNAs; • Collect X-ray diffraction data from the ribosome crystals at the APS Synchrotron; • Perform data analysis; coordinate, analyze, and document results for publication; • Directly participate in writing papers and grants based on the experimental data; • Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry; • Attend weekly group meetings and journal clubs. *Minimum qualifications:* • Bachelor’s degree in chemistry, biochemistry, biophysics, or a related field; • Master’s degree or higher is preferred; • Minimum 3 years of laboratory research experience; • Strong background in biochemistry and molecular biology; • Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); • Experience in structural biology (cryo-EM or X-ray crystallography) is desired; • Experience in RNA biology is desired. • The successful candidate should be able to walk into the laboratory and be able to start working without significant additional training in basic molecular biology techniques. *For fullest consideration, interested candidates should submit an application, including CV, cover letter, and contact information for three references at https://jobs.uic.edu/job-board/job-details?jobID=149023 <https://jobs.uic.edu/job-board/job-details?jobID=149023> by August 9, 2021. Questions can be directed to Dr. Polikanov at yuryp(a)uic.edu <yuryp(a)uic.edu>. **In the cover letter, describe what your scientific interests are and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group.* *The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer including Disability/Vets.* *Offers of employment by the University of Illinois may be subject to approval by the University’s Board of Trustees and are made contingent upon the candidate’s successful completion of any criminal background checks and other pre-employment assessments that may be required for the position being offered. Additional information regarding such pre-employment checks and assessments may be provided as applicable during the hiring process.* *The University of Illinois System requires candidates selected for hire to disclose any documented finding of sexual misconduct or sexual harassment and to authorize inquiries to current and former employers regarding findings of sexual misconduct or sexual harassment. For more information, visit https://www.hr.uillinois.edu/cms/One.aspx <https://www.hr.uillinois.edu/cms/One.aspx>? portalId=4292&pageId=1411899* -- ------------------------------ Yury Polikanov, Ph.D. Associate Professor Department of Biological Sciences College of Liberal Arts and Sciences University of Illinois at Chicago 900 South Ashland Avenue, MBRB 4170 Chicago, IL 60607 Tel: 1-312-413-2408 (Office) Tel: 1-312-355-0463 (Laboratory) Fax: 1-312-413-2691 E-mail: yuryp(a)uic.edu Web-Page: *http://bios.uic.edu/bios/people/faculty/yury-polikanov <http://bios.uic.edu/bios/people/faculty/yury-polikanov>* [image: Image result for uic logo] ------------------------------

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Job opening: Scientist, Computational Chemistry
by Ying Zhang 26 Jul '21

26 Jul '21

Dear all, This post is to bring your attention to a job opportunity of a scientist position at Plexxikon Inc. We are looking for a highly motivated, computational chemist with expertise in protein structure predictions/modeling. Experience with small molecule design is a plus, but not required. Please help to distribute this to anyone that might be interested. Plexxikion (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/apply_flow/standard_applications/apply?job_id=… Please apply through the link, but not reply to this email. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

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error in Download Request Form for Non-Profit Institutions
by Maxime Cuypers, Ph.D. 26 Jul '21

26 Jul '21

Hello, i get the following error: The server encountered an internal error and was unable to complete your request. Error message: The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there was an error in a CGI script. tried multiple times in firefox. any idea what causes this? cheers, Dr. Maxime Cuypers Researcher, Structural Biology, St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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Problem in real space
by Firdous Tarique 26 Jul '21

26 Jul '21

Hi I am getting the following error during real space refinement of the model and map. Can anybody suggest what it is actually about. It is something about geometry_restraints but I am not able to figure it out where. Can we do something in refinement settings Or change any threshold value to avoid these problems? Input is 80S.pdb ribosome and its corresponding em map. File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1486, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1388, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1269, in check_bonded_distance_cutoff raise RuntimeError(msg) Best regards Firdous

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post-doc position at KU Leuven, ligand-gated ion channels
by Chris Ulens 26 Jul '21

26 Jul '21

A post-doctoral position is available at the Laboratory of Prof. Chris Ulens, KU Leuven, Belgium (http://www.xtal.be). The research in the Laboratory of Structural Neurobiology is aimed at understanding the molecular mechanism of ligand-gated ion channels. Our methods rely on X-ray crystallography and cryo-EM in combination with electrophysiological recordings and fluorescence-based techniques. Our laboratory hosts an integrated macromolecular crystallization facility with a Mosquito crystallization robot and two RockImagers. We have access to a 200 kV Glacios microscope on campus as well as 300 kV JEOL CryoARM300 at the nearby EM facility in Brussels. Current projects are situated at the crossroads of structural elucidation and drug discovery of different pentameric ligand-gated ion channels. We would like to recruit a post-doc with prior experience in cryo-EM or X-ray crystallography of membrane proteins. The successful candidate: - easily communicates in an open verbal manner and has a team player spirit - has an ambitious work ethic - critically contributes to writing of manuscripts and grant proposals - makes efforts to obtain independent funding - meets intermediate deadlines and brings projects to a successful end - fuels internal discussions of recent publications in the field - sets an example to younger PhD students in the lab - identifies directions for future scientific research The position is open immediately and applications will be accepted until the position is filled. Applicants are requested to submit a CV with publication list and two references. E-mail to chris.ulens(a)kuleuven.be Selection of recent publications: A lipid site shapes the agonist response of a pentameric ligand-gated ion channel. Hénault CM, Govaerts C, Spurny R, Brams M, Estrada-Mondragon A, Lynch J, Bertrand D, Pardon E, Evans GL, Woods K, Elberson BW, Cuello LG, Brannigan G, Nury H, Steyaert J, Baenziger JE, Ulens C. Nat Chem Biol. 2019;15(12):1156-1164. doi: 10.1038/s41589-019-0369-4. Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT3 receptor via a common vestibule site. Brams M, Govaerts C, Kambara K, Price KL, Spurny R, Gharpure A, Pardon E, Evans GL, Bertrand D, Lummis SC, Hibbs RE, Steyaert J, Ulens C. Elife. 2020;9:e51511. doi: 10.7554/eLife.51511. The structural basis for an on-off switch controlling Gβγ-mediated inhibition of TRPM3 channels. Behrendt M, Gruss F, Enzeroth R, Dembla S, Zhao S, Crassous PA, Mohr F, Nys M, Louros N, Gallardo R, Zorzini V, Wagner D, Economou A, Rousseau F, Schymkowitz J, Philipp SE, Rohacs T, Ulens C, Oberwinkler J. Proc Natl Acad Sci U S A. 2020;117(46):29090-29100. doi: 10.1073/pnas.2001177117.

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Move fem map back to protein?
by Murpholino Peligro 23 Jul '21

23 Jul '21

Dear all.. How do I move a fem map back to the protein molecule? I did `phenix.fem PHASER.1-coot-1_refine_001.pdb PHASER.1-coot-0_refine_data.mtz` to generate the fem map, but when I open with coot `coot PHASER.1-coot-1_refine_001.mtz PHASER.1-coot-1_refine_001.pdb` and then file->open map->fem.cpp4... the fem map does not cover the protein (as shown in .png attached) I am not sure if this is phenix (a missing option?) or coot related ... thanks

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Ligand Library
by Christian Tüting 22 Jul '21

22 Jul '21

Dear Phenix-Team, dear Mailing-List, I have a question regarding bound ligands during refinement. In our initial structure, we have multiple spheroidenes bound (pdb ligand id SPO), but experimental data suggest that it should be speroidenones (pdb ligand id SPN). The difference between these molecules are located in an additional oxygen at the head group and a different saturation level of the carbon chain. I mananged to exchange the molecule using Coot, but during refinement I got following error: Number of atoms with unknown nonbonded energy type symbols: 602 "HETATM18420 C1 SPN B 600 .*.N C " "HETATM18421 C10 SPN B 600 .*.N C " "HETATM18422 C11 SPN B 600 .*.N C " "HETATM18423 C12 SPN B 600 .*.N C " "HETATM18424 C13 SPN B 600 .*.N C " "HETATM18425 C14 SPN B 600 .*.N C " "HETATM18426 C15 SPN B 600 .*.N C " "HETATM18427 C16 SPN B 600 .*.N C " "HETATM18428 C17 SPN B 600 .*.N C " "HETATM18429 C18 SPN B 600 .*.N C " ... (remaining 592 not shown) So, as far as I understand this error, the ligand is not in the restrained in the ligand library. I followed this tutorial: https://phenix-online.org/documentation/tutorials/elbow.html to generate the .cif file for refinement. I was just using the pdb file and the geometry from there, as it was "coot-refined" and thereby I expected the correct conformation. The refinement than run fine, but the ligand after refinement is in a complete wrong conformation and parts of the carbon chain is outside the density. I am not sure, if this is due to low resolution at these regions (which are indeed very low compared to other ligands or proteins in the map), or if during restraining something went wrong. Is it possible to add this ligand to the phenix ligand library or do you have any suggestions, how to improve the restraining using the elbow tool? Thanks in advance Christian Tüting Dr. rer. nat. Christian Tüting Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.19 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524985 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Two positions (postdoc and PhD) in Structures of Metabolite Transporting Membrane Proteins at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 14 Jul '21

14 Jul '21

Dear all, Just a reminder that we have two open positions (1 postdoc and 1 PhD) available to join our team and investigate metabolite transport using structural biology. Please pass along to anyone who might be interested. Thanks! PhD position = https://bit.ly/3Ak5Far Postdoc position = https://bit.ly/2SXS7Rm /Bjørn ----------------------------------------------------------------------- STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in metabolite transport A PhD and a postdoc position are available in membrane protein biochemistry and structural biology in the research group of Dr. Bjørn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective (see http://pedersenlab.dk). The projects will be developed in discussion with the selected candidates, but will involve expression, purification and structural/functional characterization of membrane proteins involved in metabolite uptake. Example see https://pubmed.ncbi.nlm.nih.gov/31543266/. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. The projects are fully funded by the European Research Council (ERC). The candidates should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified, but start date is negotiable. The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university.

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geometry_minimization makes molprobity score worse
by James Holton 13 Jul '21

13 Jul '21

Greetings all, and I hope this little observation helps improve things somehow. I did not expect this result, but there it is. My MolProbity score goes from 0.7 to 1.9 after a run of phenix.geometry_minimization I started with an AMBER-minimized model (based on 1aho), and that got me my best MolProbity score so far (0.7). But, even with hydrogens and waters removed the geometry_minimization run increases the clashscore from 0 to 3.1 and Ramachandran favored drops from 98% to 88% with one residue reaching the outlier level. Just for comparison, with refmac5 in "refi type ideal" mode I see the MolProbity rise to 1.13, but Clashscore remains zero, some Ramas go from favored to allowed, but none rise to the level of outliers. Files and logs here: https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz I suspect this might have something to do with library values for main-chain bonds and angles? They do seem to vary between programs. Phenix having the shortest CA-CA distance by up to 0.08 A. After running thorough minimization on a poly-A peptide I get: bond amber refmac phenix shelxl Stryer C-N 1.330 1.339 1.331 1.325 1.32 N-CA 1.462 1.482 1.455 1.454 1.47 CA-C 1.542 1.534 1.521 1.546 1.53 CA-CA 3.862 3.874 3.794 3.854 So, which one is "right" ? Cheers, -James

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