+Open data
-Basic information
Entry | Database: PDB / ID: 3w5h | ||||||
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Title | Ultra-high resolution structure of NADH-cytochrome b5 reductase | ||||||
Components | NADH-cytochrome b5 reductase 3 | ||||||
Keywords | OXIDOREDUCTASE / Electron transfer / FAD binding / ER | ||||||
Function / homology | Function and homology information cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / cholesterol biosynthetic process / FAD binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / endoplasmic reticulum membrane / mitochondrion Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.78 Å | ||||||
Authors | Takeda, K. / Ohno, H. / Kosugi, M. / Takaba, K. / Miki, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w5h.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w5h.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 3w5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w5h_validation.pdf.gz | 457.7 KB | Display | wwPDB validaton report |
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Full document | 3w5h_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | 3w5h_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 3w5h_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/3w5h ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w5h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30873.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P83686, cytochrome-b5 reductase | ||
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#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% PEG 4000, 10mM potassium phosphate, 5mM dithionite, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 40 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.65 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 2, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 0.78→50 Å / Num. obs: 314321 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 0.78→0.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / Num. unique all: 11636 / % possible all: 70.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY INDH Resolution: 0.78→50 Å / Isotropic thermal model: Anisotropic / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: SHELXL-97 HAS ALSO BEEN USED IN THE REFINEMENT
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Refinement step | Cycle: LAST / Resolution: 0.78→50 Å
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