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- PDB-3w2g: Crystal structure of fully reduced form of NADH-cytochrome b5 red... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w2g | ||||||
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Title | Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver | ||||||
![]() | NADH-cytochrome b5 reductase 3 | ||||||
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Function / homology | ![]() cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / cholesterol biosynthetic process / FAD binding / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, M. / Tamada, T. / Matsumoto, F. / Shoyama, Y. / Kimura, S. / Kuroki, R. / Miki, K. | ||||||
![]() | ![]() Title: Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer Authors: Yamada, M. / Tamada, T. / Takeda, K. / Matsumoto, F. / Ohno, H. / Kosugi, M. / Takaba, K. / Shoyama, Y. / Kimura, S. / Kuroki, R. / Miki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.9 KB | Display | ![]() |
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PDB format | ![]() | 102.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30786.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FAD / ![]() |
#3: Chemical | ChemComp-NAD / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.64 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 70%(v/v) MPD, 0.1M HEPES-NaOH pH 6.5, 25mM NADH, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2012 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.68→50 Å / Num. obs: 42188 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.68→1.71 Å / Rmerge(I) obs: 0.373 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.84 Å2 / Biso mean: 24.0667 Å2 / Biso min: 9.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→30.822 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: 15
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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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