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- PDB-4f8y: Complex structure of NADPH:quinone oxidoreductase with menadione ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f8y | ||||||
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Title | Complex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans | ||||||
![]() | NADPH Quinone Oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / NADPH / Quinone Oxidoreductase / FAD | ||||||
Function / homology | ![]() NAD(P)H dehydrogenase (quinone) / NAD(P)H dehydrogenase (quinone) activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Z. / Li, L. / Su, X.-D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.1 KB | Display | ![]() |
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PDB format | ![]() | 142.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 40.4 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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.) ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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