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Yorodumi- PDB-1jwj: Murine Inducible Nitric Oxide Synthase Oxygenase Dimer (Delta 65)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jwj | ||||||
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Title | Murine Inducible Nitric Oxide Synthase Oxygenase Dimer (Delta 65) with W457F Mutation at Tetrahydrobiopterin Binding Site | ||||||
Components | Nitric Oxide Synthase | ||||||
Keywords | OXIDOREDUCTASE / Nitric Oxide L-Arginine Monooxygenase / Heme / Dimer / NOS | ||||||
Function / homology | Function and homology information Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / positive regulation of killing of cells of another organism / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton ...Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / positive regulation of killing of cells of another organism / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton / superoxide metabolic process / cGMP-mediated signaling / nitric-oxide synthase binding / peptidyl-cysteine S-nitrosylation / regulation of cytokine production involved in inflammatory response / cellular response to cytokine stimulus / regulation of insulin secretion / cellular response to organic cyclic compound / nitric-oxide synthase (NADPH) / blood vessel remodeling / nitric oxide mediated signal transduction / response to tumor necrosis factor / nitric-oxide synthase activity / arginine catabolic process / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / positive regulation of interleukin-8 production / negative regulation of protein catabolic process / response to bacterium / regulation of blood pressure / Hsp90 protein binding / circadian rhythm / cellular response to type II interferon / beta-catenin binding / positive regulation of interleukin-6 production / cellular response to xenobiotic stimulus / FMN binding / peroxisome / NADP binding / flavin adenine dinucleotide binding / actin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / calmodulin binding / response to hypoxia / intracellular signal transduction / defense response to bacterium / cadherin binding / inflammatory response / positive regulation of apoptotic process / negative regulation of gene expression / heme binding / protein kinase binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Aoyagi, M. / Arvai, A.S. / Ghosh, S. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structures of tetrahydrobiopterin binding-site mutants of inducible nitric oxide synthase oxygenase dimer and implicated roles of Trp457. Authors: Aoyagi, M. / Arvai, A.S. / Ghosh, S. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D. #1: Journal: Biochemistry / Year: 2001 Title: A Conserved Tryptophan in Nitric Oxide Synthase Regulates Heme-dioxy Reduction by Tetrahydrobiopterin Authors: Wang, Z.-Q. / Wei, C.-C. / Ghosh, S. / Meade, A. / Hemann, C. / Hille, R. / Stuehr, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jwj.cif.gz | 194.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jwj.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jwj_validation.pdf.gz | 635.9 KB | Display | wwPDB validaton report |
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Full document | 1jwj_full_validation.pdf.gz | 650.2 KB | Display | |
Data in XML | 1jwj_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 1jwj_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/1jwj ftp://data.pdbj.org/pub/pdb/validation_reports/jw/1jwj | HTTPS FTP |
-Related structure data
Related structure data | 1jwkC 1nodS C: citing same article (ref.) 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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Details | The biological assembly is a dimer generated from each subunit, A and B, in the asymmetric unit by the operations 1+y-x, y, 1/2-z and 2-x, 1-x+y, 2/3-z+5/3. |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 50081.914 Da / Num. of mol.: 2 / Fragment: Oxygenase Domain 65-498 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / References: UniProt: P29477, nitric-oxide synthase (NADPH) #2: Sugar | |
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-Non-polymers , 5 types, 347 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: 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: 3.84 Å3/Da / Density % sol: 67.98 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Ammonium sulfate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 70 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 | |||||||||||||||||||||||||||||||||||
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 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 1999 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 142979 / Num. obs: 46998 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.04 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.07 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2 / Num. unique all: 4115 / Rsym value: 0.45 / % possible all: 87 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 142979 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 87 % / Rmerge(I) obs: 0.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NOD Resolution: 2.6→49.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 769561.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.9435 Å2 / ksol: 0.320533 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→49.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 47.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.383 / % reflection Rfree: 5 % / Rfactor Rwork: 0.357 |