+Open data
-Basic information
Entry | Database: PDB / ID: 1ja1 | ||||||
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Title | CYPOR-Triple Mutant | ||||||
Components | NADPH-Cytochrome P450 Reductase | ||||||
Keywords | OXIDOREDUCTASE / NADPH-Cytochrome P450 Reductase | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Hubbard, P.A. / Shen, A.L. / Paschke, R. / Kasper, C.B. / Kim, J.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: NADPH-cytochrome P450 oxidoreductase. Structural basis for hydride and electron transfer. Authors: Hubbard, P.A. / Shen, A.L. / Paschke, R. / Kasper, C.B. / Kim, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ja1.cif.gz | 290.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ja1.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ja1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1ja1 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1ja1 | HTTPS FTP |
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-Related structure data
Related structure data | 1j9zC 1ja0C 1amoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 70631.391 Da / Num. of mol.: 2 / Mutation: S457A/C630A/D675N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CYPOR / Plasmid: pOR263 / Production host: Escherichia coli (E. coli) / Strain (production host): C1A / References: UniProt: P00388, NADPH-hemoprotein reductase |
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-Non-polymers , 5 types, 1133 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EPE / | #6: 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: 2.45 Å3/Da / Density % sol: 49.79 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, Hepes, Sodium Acetate, NADP+, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 1999 / Details: mirrors |
Radiation | Monochromator: bent conical Si-mirror (Rh coating) + bent cylindrical Ge(111) monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 129222 / Num. obs: 120472 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 15.6 Å2 / Limit h max: 56 / Limit h min: 0 / Limit k max: 64 / Limit k min: 0 / Limit l max: 65 / Limit l min: 0 / Observed criterion F max: 473892.21 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4536 / Rsym value: 0.285 / % possible all: 70.8 |
Reflection | *PLUS Num. measured all: 1504516 |
Reflection shell | *PLUS % possible obs: 70.8 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 1AMO Resolution: 1.8→29.16 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 42.1015 Å2 / ksol: 0.330899 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.1 Å2 / Biso mean: 34.95 Å2 / Biso min: 9.58 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.16 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.338 / % reflection Rfree: 3.6 % / Rfactor Rwork: 0.338 |