+Open data
-Basic information
Entry | Database: PDB / ID: 4n9q | ||||||
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Title | Crystal structure of paAzoR1 bound to ubiquinone-1 | ||||||
Components | FMN-dependent NADH-azoreductase 1 | ||||||
Keywords | OXIDOREDUCTASE / azoreductase / quinone / NAD(P)H quinone oxidoreductase / ubiquinone-1 | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / NADPH:quinone reductase activity / 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Ryan, A. / Kaplan, E. / Crescente, V. / Lowe, E. / Preston, G.M. / Sim, E. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Identification of NAD(P)H Quinone Oxidoreductase Activity in Azoreductases from P. aeruginosa: Azoreductases and NAD(P)H Quinone Oxidoreductases Belong to the Same FMN-Dependent Superfamily of Enzymes. Authors: Ryan, A. / Kaplan, E. / Nebel, J.C. / Polycarpou, E. / Crescente, V. / Lowe, E. / Preston, G.M. / Sim, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n9q.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n9q.ent.gz | 187.1 KB | Display | PDB format |
PDBx/mmJSON format | 4n9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n9q_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4n9q_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4n9q_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 4n9q_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/4n9q ftp://data.pdbj.org/pub/pdb/validation_reports/n9/4n9q | HTTPS FTP |
-Related structure data
Related structure data | 4n65C 2v9cS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23077.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 /PAO1 /1C /PRS 101 /LMG 12228 / Gene: azoR1, PA0785 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plyss References: UniProt: Q9I5F3, Oxidoreductases; Acting on other nitrogenous compounds as donors |
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-Non-polymers , 5 types, 161 molecules
#2: Chemical | #3: Chemical | ChemComp-UQ1 / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-SO4 / | #6: 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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 1.6 M ammonium sulphate, 0.1 M HEPES pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8726 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 2, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→71.362 Å / Num. all: 26575 / Num. obs: 26575 / % possible obs: 90.7 % / Redundancy: 4.7 % / Rsym value: 0.053 / Net I/σ(I): 17.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2V9C Resolution: 2→43.18 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7707 / SU ML: 0.26 / σ(F): 1.36 / Phase error: 27.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.56 Å2 / Biso mean: 49.2038 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.18 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 24.7322 Å / Origin y: -13.6114 Å / Origin z: 11.766 Å
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Refinement TLS group |
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