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Yorodumi- PDB-1amo: THREE-DIMENSIONAL STRUCTURE OF NADPH-CYTOCHROME P450 REDUCTASE: P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1amo | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF NADPH-CYTOCHROME P450 REDUCTASE: PROTOTYPE FOR FMN-AND FAD-CONTAINING ENZYMES | ||||||
Components | NADPH-CYTOCHROME P450 REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / NITRIC OXIDE SYNTHASE | ||||||
Function / homology | Function and homology information iron-cytochrome-c reductase activity / nitrate catabolic process / cellular organofluorine metabolic process / demethylation / carnitine metabolic process / flavonoid metabolic process / nitric oxide dioxygenase NAD(P)H activity / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / nitric oxide catabolic process ...iron-cytochrome-c reductase activity / nitrate catabolic process / cellular organofluorine metabolic process / demethylation / carnitine metabolic process / flavonoid metabolic process / nitric oxide dioxygenase NAD(P)H activity / 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 / 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 nutrient / response to hormone / electron transport chain / FMN binding / NADP binding / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer 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 / MIR / Resolution: 2.6 Å | ||||||
Authors | Wang, M. / Roberts, D.L. / Paschke, R. / Shea, T.M. / Masters, B.S.S. / Kim, J.J.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes. Authors: Wang, M. / Roberts, D.L. / Paschke, R. / Shea, T.M. / Masters, B.S. / 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 | 1amo.cif.gz | 257.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1amo.ent.gz | 205.9 KB | Display | PDB format |
PDBx/mmJSON format | 1amo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1amo_validation.pdf.gz | 816.8 KB | Display | wwPDB validaton report |
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Full document | 1amo_full_validation.pdf.gz | 855.3 KB | Display | |
Data in XML | 1amo_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 1amo_validation.cif.gz | 44.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/1amo ftp://data.pdbj.org/pub/pdb/validation_reports/am/1amo | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99752, -0.00364, 0.07025), Vector: |
-Components
#1: Protein | Mass: 69971.641 Da / Num. of mol.: 2 / Fragment: HYDROPHILIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: MITOCHONDRIA / Organ: LIVER / Production host: Escherichia coli (E. coli) / 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: 2.49 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / pH: 6.5 / Method: vapor diffusionDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 17, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 41132 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.07 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.308 / % possible all: 85.8 |
Reflection | *PLUS Num. measured all: 171499 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 85.8 % / Rmerge(I) obs: 0.308 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.6→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 26.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.29 |