+Open data
-Basic information
Entry | Database: PDB / ID: 7thg | ||||||
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Title | Crystal Structure Of Human NADH-Cytochrome B5 Reductase | ||||||
Components | NADH-cytochrome b5 reductase 3 soluble form | ||||||
Keywords | FLAVOPROTEIN / FAD / B5R / Reductase / NADH | ||||||
Function / homology | Function and homology information nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / AMP binding / hemoglobin complex / cholesterol biosynthetic process / nitric oxide biosynthetic process ...nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / AMP binding / hemoglobin complex / cholesterol biosynthetic process / nitric oxide biosynthetic process / FAD binding / lipid droplet / mitochondrial membrane / ADP binding / NAD binding / azurophil granule lumen / mitochondrial outer membrane / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / extracellular region / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Zheng, A. / Thibodeau, P.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Structure Of wild-type Human NADH-Cytochrome B5 Reductase and mutants Authors: Zheng, A. / Thibodeau, P.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7thg.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7thg.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 7thg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7thg_validation.pdf.gz | 735.3 KB | Display | wwPDB validaton report |
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Full document | 7thg_full_validation.pdf.gz | 742.1 KB | Display | |
Data in XML | 7thg_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 7thg_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/7thg ftp://data.pdbj.org/pub/pdb/validation_reports/th/7thg | HTTPS FTP |
-Related structure data
Related structure data | 7tnvC 7tswC 1umkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31151.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00387 |
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#2: Chemical | ChemComp-FAD / |
Has ligand of interest | Y |
-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: 48.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4K 30%, 0.1M Na/K PO4 pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.05 Å / Num. obs: 6909 / % possible obs: 98.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 67.43 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.054 / Rrim(I) all: 0.13 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 6.03 % / Rmerge(I) obs: 1.207 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 659 / CC1/2: 0.659 / Rpim(I) all: 0.536 / Rrim(I) all: 1.323 / % possible all: 96.63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UMK Resolution: 2.9→32.41 Å / SU ML: 0.4535 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.524 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→32.41 Å
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Refine LS restraints |
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LS refinement shell |
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