+Open data
-Basic information
Entry | Database: PDB / ID: 7awv | ||||||
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Title | Azoreductase (AzoRo) from Rhodococcus opacus 1CP | ||||||
Components | FMN-dependent NADH-azoreductase | ||||||
Keywords | OXIDOREDUCTASE / azoreductase / Actinobacterium / dye degradation / NADH-quinone oxido-reductase | ||||||
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 Similarity search - Function | ||||||
Biological species | Rhodococcus opacus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bento, I. / Ngo, A. / Qi, J. / Juric, C. / Tischler, D. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2022 Title: Identification of molecular basis that underlie enzymatic specificity of AzoRo from Rhodococcus opacus 1CP: A potential NADH:quinone oxidoreductase. Authors: Ngo, A.C.R. / Qi, J. / Juric, C. / Bento, I. / Tischler, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7awv.cif.gz | 305.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7awv.ent.gz | 244.3 KB | Display | PDB format |
PDBx/mmJSON format | 7awv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7awv_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7awv_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7awv_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 7awv_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/7awv ftp://data.pdbj.org/pub/pdb/validation_reports/aw/7awv | HTTPS FTP |
-Related structure data
Similar structure data |
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-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 3 - 206 / Label seq-ID: 3 - 206
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 22853.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus opacus (bacteria) / Gene: azoR, R1CP_39980 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1B1KJ01, FMN-dependent NADH-azoreductase #2: Chemical | #3: Chemical | ChemComp-IPA / | #4: Chemical | ChemComp-PEG / #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: 2.55 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 16-20% of isopropanol, 12-16% PEG4000 and 0.1M of sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→70.43 Å / Num. obs: 23710 / % possible obs: 99.87 % / Redundancy: 5.6 % / Biso Wilson estimate: 39.87 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.063 / Rrim(I) all: 0.148 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.654 / Num. unique obs: 2347 / CC1/2: 0.53 / CC star: 0.832 / Rpim(I) all: 0.795 / Rrim(I) all: 1.84 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: homology model Resolution: 2.2→70.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.691 / SU ML: 0.256 / Cross valid method: FREE R-VALUE / ESU R: 0.293 / ESU R Free: 0.225 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→70.33 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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