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Yorodumi- PDB-4bo8: Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bo8 | ||||||
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Title | Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 1-(2-amino-4- phenylimidazol-1-yl)-3-(2-fluorophenyl)urea at 2.7A 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: 2.7 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 | 4bo8.cif.gz | 343.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bo8.ent.gz | 283.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bo8_validation.pdf.gz | 1007.3 KB | Display | wwPDB validaton report |
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Full document | 4bo8_full_validation.pdf.gz | 1019.1 KB | Display | |
Data in XML | 4bo8_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 4bo8_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/4bo8 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/4bo8 | HTTPS FTP |
-Related structure data
Related structure data | 4afnC 4ag3C 4bntC 4bnuC 4bnvC 4bnwSC 4bnxC 4bnyC 4bnzC 4bo0C 4bo1C 4bo2C 4bo3C 4bo4C 4bo5C 4bo6C 4bo7C 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: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Nonpolymer details | 34X: THE LIGAND 1-(2-AMINO-4-PHENYLIMIDAZOL-1-YL)-3-(2- FLUOROPHENYL)UREA IS BOUND AT THE ...34X: THE LIGAND 1-(2-AMINO-4-PHENYLIMID | |
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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: 1.93 Å3/Da / Density % sol: 36.3 % / Description: LIGAND FREE PDB |
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Crystal grow | pH: 6.5 Details: 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M SODIUM CHLORIDE, 2 M AMMONIUM SULPHATE, 1MM 1-(2-AMINO- 4-PHENYLIMIDAZOL-1-YL)-3-(2-FLUOROPHENYL)UREA, FINAL PROTEIN CONCENTRATION 5 MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2012 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→37.08 Å / Num. obs: 23723 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BNW Resolution: 2.7→37.11 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.793 / SU B: 34.653 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / 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: 29.599 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→37.11 Å
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Refine LS restraints |
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