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Yorodumi- PDB-7tnv: Crystal Structure Of Human NADH-Cytochrome B5 Reductase T117S Mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tnv | ||||||
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Title | Crystal Structure Of Human NADH-Cytochrome B5 Reductase T117S Mutant | ||||||
Components | NADH-cytochrome b5 reductase 3 soluble form | ||||||
Keywords | OXIDOREDUCTASE / FAD / B5R / Reductase / T117S | ||||||
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: 1.93 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 | 7tnv.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tnv.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 7tnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tnv_validation.pdf.gz | 786.5 KB | Display | wwPDB validaton report |
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Full document | 7tnv_full_validation.pdf.gz | 787.8 KB | Display | |
Data in XML | 7tnv_validation.xml.gz | 15 KB | Display | |
Data in CIF | 7tnv_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/7tnv ftp://data.pdbj.org/pub/pdb/validation_reports/tn/7tnv | HTTPS FTP |
-Related structure data
Related structure data | 7thgC 7tswC 1umkS C: citing same article (ref.) S: Starting model for refinement |
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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: 31137.947 Da / Num. of mol.: 1 / Mutation: T117S 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 / |
#3: Water | ChemComp-HOH / |
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: 2.48 Å3/Da / Density % sol: 50.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 7.8, PEG 4K 10% |
-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 27, 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: 1.93→46.34 Å / Num. obs: 22991 / % possible obs: 99.8 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.073 / Net I/av σ(I): 23.58 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.93→1.98 Å / Mean I/σ(I) obs: 2.55 / Num. unique obs: 1640 / CC1/2: 0.809 / Rrim(I) all: 1.602 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1umk Resolution: 1.93→46.34 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5508 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: 35.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→46.34 Å
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Refine LS restraints |
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LS refinement shell |
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