+Open data
-Basic information
Entry | Database: PDB / ID: 6njr | ||||||
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Title | Spin-Labeled T177C/A637C Mutant of Rat CYPOR | ||||||
Components | NADPH--cytochrome P450 reductase | ||||||
Keywords | FLAVOPROTEIN / OXIDOREDUCTASE / CYPOR / Cysless / SDSL / site-directed spin-labeling | ||||||
Function / homology | Function and homology information iron-cytochrome-c reductase activity / nitrate catabolic process / cellular organofluorine metabolic process / demethylation / nitric oxide dioxygenase NAD(P)H activity / carnitine metabolic process / flavonoid metabolic process / nitric oxide catabolic process / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation ...iron-cytochrome-c reductase activity / nitrate catabolic process / cellular organofluorine metabolic process / demethylation / nitric oxide dioxygenase NAD(P)H activity / carnitine metabolic process / flavonoid metabolic process / nitric oxide catabolic process / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / cytochrome-b5 reductase activity, acting on NAD(P)H / positive regulation of steroid hormone biosynthetic process / positive regulation of chondrocyte differentiation / cellular response to follicle-stimulating hormone stimulus / positive regulation of cholesterol biosynthetic process / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / regulation of cholesterol metabolic process / cellular response to peptide hormone stimulus / response to dexamethasone / fatty acid oxidation / electron transport chain / response to hormone / response to nutrient / FMN binding / flavin adenine dinucleotide binding / NADP binding / electron transfer activity / oxidoreductase activity / hydrolase activity / response to xenobiotic stimulus / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Xia, C. / Kim, J.J.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Structural and Functional Studies of the Membrane-Binding Domain of NADPH-Cytochrome P450 Oxidoreductase. Authors: Xia, C. / Shen, A.L. / Duangkaew, P. / Kotewong, R. / Rongnoparut, P. / Feix, J. / Kim, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6njr.cif.gz | 262.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6njr.ent.gz | 207.7 KB | Display | PDB format |
PDBx/mmJSON format | 6njr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/6njr ftp://data.pdbj.org/pub/pdb/validation_reports/nj/6njr | HTTPS FTP |
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-Related structure data
Related structure data | 1ja1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 70960.789 Da / Num. of mol.: 2 Mutation: C136A,T177(R1A),C228A,C363T,C445L,C472T,C566A,C630A,A637(R1A) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Por / Variant: DELTA56 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00388, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % / Description: single crystal |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 4000, SODIUM ACETATE, HEPES, PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 39289 / % possible obs: 98.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 71.9 Å2 / Rsym value: 0.09 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.7→2.75 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.622 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JA1 Resolution: 2.7→32.37 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3526693.55 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Bsol: 38.6724 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.2 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 2.7→32.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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