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Yorodumi- PDB-5gv7: Structure of NADH-cytochrome b5 reductase refined with the multip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gv7 | ||||||
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Title | Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.80 A | ||||||
Components | NADH-cytochrome b5 reductase 3 | ||||||
Keywords | OXIDOREDUCTASE / electron transfer / flavoprotein | ||||||
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: 0.8 Å | ||||||
Authors | Takaba, K. / Takeda, K. / Miki, K. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase. Authors: Takaba, K. / Takeda, K. / Kosugi, M. / Tamada, T. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gv7.cif.gz | 203.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gv7.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/5gv7 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/5gv7 | HTTPS FTP |
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-Related structure data
Related structure data | 5gv8C 1ndhS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 2.42 Å3/Da / Density % sol: 49.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 4000, DTT, K-phos buffer |
-Data collection
Diffraction | Mean temperature: 40 K Ambient temp details: The author used a cryo-stream of helium. |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.65 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 0.8→29.3 Å / Num. obs: 314475 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rsym value: 0.067 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 0.8→0.81 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NDH Resolution: 0.8→29.3 Å / Cross valid method: FREE R-VALUE Details: The model was finally refined with aspherical atomic model by using MOPRO program.
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Refinement step | Cycle: LAST / Resolution: 0.8→29.3 Å
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