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Yorodumi- PDB-4bnt: Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bnt | ||||||
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Title | Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 2-(trifluoromethyl)-1H- benzimidazole at 2.3A resolution | ||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN FOLD / FATTY ACID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cukier, C.D. / Schnell, R. / Lindqvist, Y. / Schneider, G. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Discovery of an Allosteric Inhibitor Binding Site in 3-Oxo-Acyl-Acp Reductase from Pseudomonas Aeruginosa Authors: Cukier, C.D. / Hope, A. / Elamin, A. / Moynie, L. / Schnell, R. / Schach, S. / Kneuper, H. / Singh, M. / Naismith, J. / Lindqvist, Y. / Gray, D. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bnt.cif.gz | 343.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bnt.ent.gz | 282.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bnt_validation.pdf.gz | 472.6 KB | Display | wwPDB validaton report |
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Full document | 4bnt_full_validation.pdf.gz | 482.1 KB | Display | |
Data in XML | 4bnt_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 4bnt_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/4bnt ftp://data.pdbj.org/pub/pdb/validation_reports/bn/4bnt | HTTPS FTP |
-Related structure data
Related structure data | 4afnSC 4ag3C 4bnuC 4bnvC 4bnwC 4bnxC 4bnyC 4bnzC 4bo0C 4bo1C 4bo2C 4bo3C 4bo4C 4bo5C 4bo6C 4bo7C 4bo8C 4bo9C C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 28167.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PNIC-PA2967 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O54438, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | 36E: THE LIGAND 2-(TRIFLUOROMETHYL)-1H-BENZIMIDAZOLE IS BOUND AT THE INTERFACES BETWEEN PROTEIN ...36E: THE LIGAND 2-(TRIFLUOROM | |
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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: 1.91 Å3/Da / Density % sol: 35.65 % / Description: NONE |
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Crystal grow | Details: 0.2 M SODIUM MALONATE, 20% (W/V) PEG3350, 10 MM 2-(TRIFLUOROMETHYL)-1H-BENZIMIDAZOLE, FINAL PROTEIN CONCENTRATION 5MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 29, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.08 Å / Num. obs: 38863 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AFN CHAIN A Resolution: 2.3→29.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.49 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.242 / 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: 38.876 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.1 Å
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Refine LS restraints |
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