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Yorodumi- PDB-3w79: Crystal Structure of azoreductase AzrC in complex with sulfone-mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w79 | ||||||
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Title | Crystal Structure of azoreductase AzrC in complex with sulfone-modified azo dye Orange I | ||||||
Components | FMN-dependent NADH-azoreductase | ||||||
Keywords | OXIDOREDUCTASE / azoreductase / azo bond cleavage / FMN-binding / azoreductase-azoreductase substrate complex | ||||||
Function / homology | Function and homology information 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 as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus (Bacillus rRNA group 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ogata, D. / Yu, J. / Ooi, T. / Yao, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of AzrA and of AzrC complexed with substrate or inhibitor: insight into substrate specificity and catalytic mechanism. Authors: Yu, J. / Ogata, D. / Gai, Z. / Taguchi, S. / Tanaka, I. / Ooi, T. / Yao, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w79.cif.gz | 326.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w79.ent.gz | 268.2 KB | Display | PDB format |
PDBx/mmJSON format | 3w79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w79_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 3w79_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 3w79_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 3w79_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/3w79 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/3w79 | HTTPS FTP |
-Related structure data
Related structure data | 3w77SC 3w78C 3w7aC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 2 - 211 / Label seq-ID: 2 - 211
NCS ensembles :
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-Components
#1: Protein | Mass: 22950.822 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Strain: B29 / Gene: azrC, azoR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C0STY1, Oxidoreductases; Acting on other nitrogenous compounds as donors #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-ORI / #4: 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: 2.79 Å3/Da / Density % sol: 55.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 600, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 39733 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W77 Resolution: 2.4→36.72 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.098 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.251 / 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: 34.541 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→36.72 Å
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Refine LS restraints |
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