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Yorodumi- PDB-7f76: Crystal Structure of FMN-dependent NADPH-quinone reductase (azoR)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f76 | ||||||
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Title | Crystal Structure of FMN-dependent NADPH-quinone reductase (azoR) from Bacillus cohnii | ||||||
Components | FMN-dependent NADPH-quinone reductase (azoR) | ||||||
Keywords | OXIDOREDUCTASE / Quinone reductase (azoR) / FMN / NADH | ||||||
Function / homology | NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / ISOPROPYL ALCOHOL / FMN-dependent NADH-azoreductase Function and homology information | ||||||
Biological species | Bacillus cohnii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Yoneda, K. / Sakuraba, H. / Ohshima, T. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of FMN-dependent NADPH-quinone reductase (azoR) from Bacillus cohnii Authors: Yoneda, K. / Sakuraba, H. / Ohshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f76.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f76.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 7f76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f76 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f76 | HTTPS FTP |
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-Related structure data
Related structure data | 3gfrS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21805.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cohnii (bacteria) / Gene: azoR / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A223KLJ1 #2: Chemical | #3: Chemical | ChemComp-IPA / #4: Chemical | #5: 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: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 35% 2-propanol, 0.1 M Tris/HCl (pH 8.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→50 Å / Num. obs: 45768 / % possible obs: 98.1 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.57→1.71 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1882 / Rpim(I) all: 0.343 / Rrim(I) all: 0.821 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GFR Resolution: 1.57→47.79 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.697 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.73 Å2 / Biso mean: 20.541 Å2 / Biso min: 11.82 Å2
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Refinement step | Cycle: final / Resolution: 1.57→47.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.571→1.612 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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