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Yorodumi- PDB-7oc0: Structure of Pseudomonas aeruginosa FabF mutant C164Q in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oc0 | ||||||
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Title | Structure of Pseudomonas aeruginosa FabF mutant C164Q in complex with a ligand (2S,4R)-2-(thiophen-2-yl)thiazolidine-4-carboxylic acid | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
Keywords | ANTIBIOTIC / Inhibitor / Fatty acid biosynthesis pathway | ||||||
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 PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Georgiou, C. / Brenk, R. / Espeland, L.O. / Klein, R. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Chemmedchem / Year: 2021 Title: An Experimental Toolbox for Structure-Based Hit Discovery for P. aeruginosa FabF, a Promising Target for Antibiotics. Authors: Espeland, L.O. / Georgiou, C. / Klein, R. / Bhukya, H. / Haug, B.E. / Underhaug, J. / Mainkar, P.S. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oc0.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oc0.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 7oc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/7oc0 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/7oc0 | HTTPS FTP |
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-Related structure data
Related structure data | 7oc1C 4jb6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43322.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: fabF1, PA2965 / Cell (production host): Rosetta(DE3)pLysS Competent Cells / Production host: Escherichia coli (E. coli) References: UniProt: G3XDA2, beta-ketoacyl-[acyl-carrier-protein] synthase II #2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-MG / | #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: 2.2 Å3/Da / Density % sol: 44.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: G3XDA2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→48.5 Å / Num. obs: 63035 / % possible obs: 85.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.78→1.84 Å / Rmerge(I) obs: 0.36 / Num. unique obs: 2473 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JB6 Resolution: 1.78→48.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.337 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.099 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→48.5 Å
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Refine LS restraints |
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