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Yorodumi- PDB-8cn2: Pa.FabF-C164Q in complex with N-isobutyl-1H-pyrazole-3-carboxamide -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cn2 | ||||||
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Title | Pa.FabF-C164Q in complex with N-isobutyl-1H-pyrazole-3-carboxamide | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
Keywords | TRANSFERASE / inhibitor / FabF / 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: 1.88 Å | ||||||
Authors | Georgiou, C. / Brenk, R. | ||||||
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 | 8cn2.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cn2.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 8cn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cn2_validation.pdf.gz | 862.6 KB | Display | wwPDB validaton report |
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Full document | 8cn2_full_validation.pdf.gz | 876.6 KB | Display | |
Data in XML | 8cn2_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 8cn2_validation.cif.gz | 50.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/8cn2 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/8cn2 | HTTPS FTP |
-Related structure data
Related structure data | 8cn4C 8cn5C 8cn7C 8cn8C 8cneC 8cngC 8couC 8covC 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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-Components
#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 #2: Chemical | ChemComp-DMS / #3: Chemical | #4: 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: 2.18 Å3/Da / Density % sol: 43.67 % |
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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: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 1.878→82.57 Å / Num. obs: 60857 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.979 / Rmerge(I) obs: 0.297 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.878→1.911 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.311 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3032 / CC1/2: 0.628 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→69.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.45 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.89 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→69.4 Å
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Refine LS restraints |
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