+Open data
-Basic information
Entry | Database: PDB / ID: 4nbv | ||||||
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Title | Crystal structure of FabG from Cupriavidus taiwanensis | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein | ||||||
Keywords | OXIDOREDUCTASE / reductase | ||||||
Function / homology | Function and homology information : / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity Similarity search - Function | ||||||
Biological species | Cupriavidus taiwanensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.645 Å | ||||||
Authors | Pereira, J.H. / Mcandrew, R.P. / Javidpour, P. / Beller, H.R. / Adams, P.D. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2014 Title: Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions. Authors: Javidpour, P. / Pereira, J.H. / Goh, E.B. / McAndrew, R.P. / Ma, S.M. / Friedland, G.D. / Keasling, J.D. / Chhabra, S.R. / Adams, P.D. / Beller, H.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nbv.cif.gz | 283.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nbv.ent.gz | 237 KB | Display | PDB format |
PDBx/mmJSON format | 4nbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/4nbv ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nbv | HTTPS FTP |
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-Related structure data
Related structure data | 4nbtC 4nbuC 4nbwC 1q7bS S: Starting model for refinement C: citing same article (ref.) |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25771.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus taiwanensis (bacteria) / Strain: R1 / LMG 19424 / Gene: RALTA_A2639 / Production host: Escherichia coli (E. coli) References: UniProt: B3R6T4, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | ChemComp-B3P / | #3: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.1 Sodium Malonate pH 7.0, 0.03 M Citric Acid, 0.07 M Bis-Tris propane pH 7.6 and 20 % PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2012 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→37.325 Å / Num. all: 58825 / Num. obs: 58825 / % possible obs: 95.95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.645→1.6857 Å / % possible all: 95.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q7B Resolution: 1.645→35.403 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 14.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.645→35.403 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.3849 Å / Origin y: 39.9217 Å / Origin z: 24.1435 Å
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Refinement TLS group | Selection details: all |