[English] 日本語
Yorodumi- PDB-3wkt: Complex structure of an open form of NADPH-cytochrome P450 reduct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wkt | ||||||
---|---|---|---|---|---|---|---|
Title | Complex structure of an open form of NADPH-cytochrome P450 reductase and heme oxygenase-1 | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / Heme degradation / Microsomal membrane | ||||||
Function / homology | Function and homology information iron-cytochrome-c reductase activity / Regulation of HMOX1 expression and activity / nitrate catabolic process / cellular organofluorine metabolic process / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / demethylation / response to 3-methylcholanthrene / Heme degradation / carnitine metabolic process ...iron-cytochrome-c reductase activity / Regulation of HMOX1 expression and activity / nitrate catabolic process / cellular organofluorine metabolic process / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / demethylation / response to 3-methylcholanthrene / Heme degradation / carnitine metabolic process / flavonoid metabolic process / Cytoprotection by HMOX1 / nitric oxide dioxygenase NAD(P)H activity / negative regulation of mast cell degranulation / response to arachidonic acid / heme metabolic process / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / nitric oxide catabolic process / cytochrome-b5 reductase activity, acting on NAD(P)H / phospholipase D activity / heme oxygenase (biliverdin-producing) / positive regulation of steroid hormone biosynthetic process / cellular response to cisplatin / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of chondrocyte differentiation / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / cellular response to follicle-stimulating hormone stimulus / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / positive regulation of cholesterol biosynthetic process / heme catabolic process / cellular response to arsenic-containing substance / cellular response to nutrient / negative regulation of epithelial cell apoptotic process / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / cellular response to peptide hormone stimulus / epithelial cell apoptotic process / regulation of cholesterol metabolic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / response to dexamethasone / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / response to nutrient / response to hormone / caveola / liver regeneration / macroautophagy / electron transport chain / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / response to nicotine / response to hydrogen peroxide / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / FMN binding / NADP binding / cellular response to heat / flavin adenine dinucleotide binding / cellular response to hypoxia / angiogenesis / intracellular iron ion homeostasis / response to oxidative stress / negative regulation of neuron apoptotic process / oxidoreductase activity / electron transfer activity / hydrolase activity / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / structural molecule activity / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å | ||||||
Authors | Sugishima, M. / Sato, H. / Higashimoto, Y. / Harada, J. / Wada, K. / Fukuyama, K. / Noguchi, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural basis for the electron transfer from an open form of NADPH-cytochrome P450 oxidoreductase to heme oxygenase. Authors: Sugishima, M. / Sato, H. / Higashimoto, Y. / Harada, J. / Wada, K. / Fukuyama, K. / Noguchi, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wkt.cif.gz | 350.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wkt.ent.gz | 281.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wkt_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3wkt_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 3wkt_validation.xml.gz | 67 KB | Display | |
Data in CIF | 3wkt_validation.cif.gz | 87.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wkt ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wkt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
|
-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 70282.102 Da / Num. of mol.: 2 / Mutation: UNP RESIDUES 58-678 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Por / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00388, NADPH-hemoprotein reductase #2: Protein | Mass: 30612.496 Da / Num. of mol.: 2 / Mutation: UNP RESIDUES 1-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmox1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P06762, heme oxygenase (biliverdin-producing) |
---|
-Non-polymers , 4 types, 8 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.04 Å3/Da / Density % sol: 75.61 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 18% PEG 6000, 0.2M sodium acetate, 0.1M Tris-HCl, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 8, 2013 |
Radiation | Monochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 4.3→50 Å / Num. all: 26421 / Num. obs: 26421 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rsym value: 0.107 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 4.3→4.37 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.651 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ES9, 1DVE Resolution: 4.3→41.34 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.926 / SU B: 40.743 / SU ML: 0.521 / Cross valid method: THROUGHOUT / ESU R Free: 0.796 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 234.429 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.3→41.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|