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Yorodumi- PDB-4f8y: Complex structure of NADPH:quinone oxidoreductase with menadione ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f8y | ||||||
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Title | Complex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans | ||||||
Components | NADPH Quinone Oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / NADPH / Quinone Oxidoreductase / FAD | ||||||
Function / homology | Function and homology information NAD(P)H dehydrogenase (quinone) / NAD(P)H dehydrogenase (quinone) activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å | ||||||
Authors | Wang, Z. / Li, L. / Su, X.-D. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Complex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans Authors: Wang, Z. / Li, L. / Su, X.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f8y.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f8y.ent.gz | 142.9 KB | Display | PDB format |
PDBx/mmJSON format | 4f8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f8y_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4f8y_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4f8y_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 4f8y_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/4f8y ftp://data.pdbj.org/pub/pdb/validation_reports/f8/4f8y | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22828.451 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: SMU_1420 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8DTD1, NAD(P)H dehydrogenase (quinone) #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-VK3 / #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: 2.35 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: 0.2M KCl, 0.05M HEPES pH7.5, 35% v/v Pentaerythritol propoxylate(5/4 PO/OH), EVAPORATION, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.796→50 Å / Num. all: 78361 / Num. obs: 77264 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→19.959 Å / σ(F): 1.35 / Phase error: 18.94 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.566 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.796→19.959 Å
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Refine LS restraints |
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LS refinement shell |
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