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Yorodumi- PDB-4bo6: Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bo6 | ||||||
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Title | Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 2,3-dihydroindol-1-yl-(2- thiophen-3-yl-1,3-thiazol-4-yl)methanone at 2.8A 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: 2.8 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 | 4bo6.cif.gz | 343.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bo6.ent.gz | 283.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bo6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bo6_validation.pdf.gz | 971 KB | Display | wwPDB validaton report |
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Full document | 4bo6_full_validation.pdf.gz | 981 KB | Display | |
Data in XML | 4bo6_validation.xml.gz | 34 KB | Display | |
Data in CIF | 4bo6_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/4bo6 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/4bo6 | HTTPS FTP |
-Related structure data
Related structure data | 4afnC 4ag3C 4bntC 4bnuC 4bnvC 4bnwSC 4bnxC 4bnyC 4bnzC 4bo0C 4bo1C 4bo2C 4bo3C 4bo4C 4bo5C 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 | 36P: THE LIGAND 2,3-DIHYDROINDOL-1-YL-(2-THIOPHEN-3-YL-1,3- THIAZOL-4-YL)METHANONE IS BOUND AT THE ...36P: THE LIGAND 2,3-DIHYDROIND | |
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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: 1.95 Å3/Da / Density % sol: 36.81 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.24 M SODIUM MALONATE PH 7.0, 20% (W/V) PEG3350, 1 MM 2,3-DIHYDROINDOL-1-YL-(2-THIOPHEN- 3-YL-1,3-THIAZOL-4-YL)METHANONE, FINAL PROTEIN CONCENTRATION 5 MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0409 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 6, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0409 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15.93 Å / Num. obs: 19603 / % possible obs: 88.2 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 79.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BNW, LIGAND-FREE Resolution: 2.8→15.94 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.901 / SU B: 33.919 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.468 / 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: 38.305 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→15.94 Å
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Refine LS restraints |
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