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Yorodumi- PDB-8pj0: Pseudomonas aeruginosa FabF C164A mutant in complex with N-(1,5-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pj0 | ||||||
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Title | Pseudomonas aeruginosa FabF C164A mutant in complex with N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)-3-methylbutanamide | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
Keywords | TRANSFERASE / inhibitor / protein-ligand complex / FabF | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Georgiou, C. / Brenk, R. / Espeland, L.O. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Rsc Med Chem / Year: 2024 Title: Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection. Authors: Jalencas, X. / Berg, H. / Espeland, L.O. / Sreeramulu, S. / Kinnen, F. / Richter, C. / Georgiou, C. / Yadrykhinsky, V. / Specker, E. / Jaudzems, K. / Miletic, T. / Harmel, R. / Gribbon, P. / ...Authors: Jalencas, X. / Berg, H. / Espeland, L.O. / Sreeramulu, S. / Kinnen, F. / Richter, C. / Georgiou, C. / Yadrykhinsky, V. / Specker, E. / Jaudzems, K. / Miletic, T. / Harmel, R. / Gribbon, P. / Schwalbe, H. / Brenk, R. / Jirgensons, A. / Zaliani, A. / Mestres, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pj0.cif.gz | 633 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pj0.ent.gz | 518.8 KB | Display | PDB format |
PDBx/mmJSON format | 8pj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/8pj0 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/8pj0 | HTTPS FTP |
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-Related structure data
Related structure data | 8r0iC 8r1vC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43265.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabF1, PA2965 / Production host: Escherichia coli (E. coli) References: UniProt: G3XDA2, beta-ketoacyl-[acyl-carrier-protein] synthase II #2: Chemical | ChemComp-DMS / #3: Chemical | #4: Chemical | ChemComp-ZHX / ~{ Mass: 287.357 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H21N3O2 / Feature type: SUBJECT OF INVESTIGATION #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / Details: 0.20M ammonium formate and 31.2% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.976246 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976246 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.83 Å / Num. obs: 158061 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.99 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.8 % / Num. unique obs: 7870 / CC1/2: 0.99 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.83 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.7→48.83 Å
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