+Open data
-Basic information
Entry | Database: PDB / ID: 1ja0 | ||||||
---|---|---|---|---|---|---|---|
Title | CYPOR-W677X | ||||||
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 / cellular response to peptide hormone stimulus / regulation of cholesterol metabolic process / response to dexamethasone / fatty acid oxidation / response to hormone / response to nutrient / electron transport chain / 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: 2.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ja0.cif.gz | 233.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ja0.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ja0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1ja0 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1ja0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1j9zC 1ja1C 1amoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 70407.148 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | ChemComp-FMN / | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.68 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 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: 2.6→30 Å / Num. all: 42999 / Num. obs: 35363 / % possible obs: 82.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 43.2 Å2 / Limit h max: 39 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 44 / Limit l min: 0 / Observed criterion F max: 457287.56 / Observed criterion F min: 1.82 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 4 / Num. unique all: 1412 / Rsym value: 0.155 / % possible all: 66.8 |
Reflection | *PLUS Num. measured all: 305661 |
Reflection shell | *PLUS % possible obs: 66.8 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 1AMO Resolution: 2.6→30 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 21.9173 Å2 / ksol: 0.274683 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.28 Å2 / Biso mean: 45.48 Å2 / Biso min: 10.78 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.283 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.288 |