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Yorodumi- PDB-8cov: Pa.FabF-C164Q in complex with 6-chloro-2-methyl-1H-indole-5-carbo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cov | ||||||
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Title | Pa.FabF-C164Q in complex with 6-chloro-2-methyl-1H-indole-5-carboxylic acid | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
Keywords | TRANSFERASE / FabF / Pseudomonas aeruginosa / inhibitor / complex | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Georgiou, C. / Brenk, R. / Espeland, L.O. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Chemrxiv / Year: 2023 Title: New starting points for antibiotics targeting P. aeruginosa FabF discovered by crystallographic fragment screening followed by hit expansion Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhinsky, V. / Haug, B.E. / Mainkar, P. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cov.cif.gz | 177 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cov.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 8cov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/8cov ftp://data.pdbj.org/pub/pdb/validation_reports/co/8cov | HTTPS FTP |
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-Related structure data
Related structure data | 8cn2C 8cn4C 8cn5C 8cn7C 8cn8C 8cneC 8cngC 8couC 8pd1C 8pfzC 8qerC 8qm1C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 413 / Label seq-ID: 1 - 412
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43322.715 Da / Num. of mol.: 2 / Mutation: C164Q 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 |
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-Non-polymers , 5 types, 453 molecules
#2: Chemical | ChemComp-DMS / #3: Chemical | #4: Chemical | ChemComp-FMT / | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.22 Å3/Da / Density % sol: 44.47 % |
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Crystal grow | Temperature: 298 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: ESRF / Beamline: ID23-1 / Wavelength: 0.976252 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976252 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→82.29 Å / Num. obs: 68897 / % possible obs: 98.1 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 21137 / CC1/2: 0.797 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→51.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.098 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.115 / 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: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.768 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→51.22 Å
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Refine LS restraints |
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