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Yorodumi- PDB-2d5i: The crystal structure of AzoR (Azo Reductase) from Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d5i | ||||||
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Title | The crystal structure of AzoR (Azo Reductase) from Escherichia coli | ||||||
Components | Azo Reductase | ||||||
Keywords | OXIDOREDUCTASE / azo reductase | ||||||
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: 2.2 Å | ||||||
Authors | Ito, K. / Tanokura, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Three-dimensional structure of AzoR from Escherichia coli. An oxidereductase conserved in microorganisms Authors: Ito, K. / Nakanishi, M. / Lee, W.C. / 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 | 2d5i.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d5i.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 2d5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d5i ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d5i | HTTPS FTP |
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-Related 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) / Strain: K12 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41407, EC: 1.7.1.6 | ||
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#2: Chemical | ChemComp-FMN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.23 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→67.42 Å / Num. obs: 12145 |
-Processing
Software | Name: REFMAC / Version: 5.1.24 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→67.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.333 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.176 / 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: 28.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→67.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20 /
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