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Yorodumi- PDB-2z9c: The crystal structure of AzoR (azoreductase) from Escherichia col... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z9c | ||||||
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Title | The crystal structure of AzoR (azoreductase) from Escherichia coli: AzoR in complex with dicoumarol | ||||||
Components | FMN-dependent NADH-azoreductase | ||||||
Keywords | OXIDOREDUCTASE / azoreductase / Flavoprotein / FMN / NAD | ||||||
Function / homology | Function and homology information azobenzene reductase activity / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / response to oxidative stress / electron transfer activity / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ito, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Expansion of Substrate Specificity and Catalytic Mechanism of Azoreductase by X-ray Crystallography and Site-directed Mutagenesis Authors: Ito, K. / Nakanishi, M. / Lee, W.C. / Zhi, Y. / Sasaki, H. / Zenno, S. / Saigo, K. / Kitade, Y. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z9c.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z9c.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 2z9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/2z9c ftp://data.pdbj.org/pub/pdb/validation_reports/z9/2z9c | HTTPS FTP |
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-Related structure data
Related structure data | 2z98C 2z9bC 2z9dC 1v4bS 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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-Components
#1: Protein | Mass: 21547.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: azoR / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P41407, EC: 1.7.1.6 |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-DTC / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.89 Å / Num. obs: 9493 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1V4B Resolution: 2.3→19.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.093 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.234 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.175 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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