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Yorodumi- PDB-7n2x: The crystal structure of an FMN-dependent NADH:quinone oxidoreduc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n2x | ||||||
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Title | The crystal structure of an FMN-dependent NADH:quinone oxidoreductase, AzoR from Escherichia coli | ||||||
Components | FMN-dependent NADH:quinone oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / FMN / NADH / Azoreductase / AzoR | ||||||
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 | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Arcinas, A.J. / Fedorov, E. / Kelly, L. / Almo, S.C. / Ghosh, A. | ||||||
Citation | Journal: To Be Published Title: Uncovering a novel mechanism of enzyme activation in multimeric azoreductases Authors: Hitchings, R. / Ryan, A. / Arcinas, A.J. / Ghosh, A. / Almo, S.C. / Kelly, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n2x.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n2x.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 7n2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/7n2x ftp://data.pdbj.org/pub/pdb/validation_reports/n2/7n2x | HTTPS FTP |
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-Related structure data
Related structure data | 7n2wC 1v4bS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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, 1 molecules A
#1: Protein | Mass: 24225.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: azoR, Z2315, ECs2014 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8X9S9, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor, FMN-dependent NADH-azoreductase |
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-Non-polymers , 5 types, 180 molecules
#2: Chemical | ChemComp-FMN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-DHA / | #5: Chemical | ChemComp-P4G / | #6: Water | ChemComp-HOH / | |
-Details
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: 2.44 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.02 M Magnesium Chloride, 0.1 M HEPES pH 7.5, 22 %(w/v) Polyacrylic Acid 5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2017 / Details: KB MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.83 Å / Num. obs: 26943 / % possible obs: 99.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 23.13 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.65 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V4B Resolution: 1.7→19.83 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.22 / 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 mean: 30.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.83 Å
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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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