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Yorodumi- PDB-1dww: MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER N-hydroxya... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dww | ||||||
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Title | MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER N-hydroxyarginine and dihydrobiopterin | ||||||
Components | NITRIC OXIDE SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE/TRANSFERASE / COMPLEX (OXIDOREDUCTASE-TRANSFERASE) / NITRIC OXIDE MONOOXYGENASE / HEME / DIMER / INTERMEDIATE / PTERIN / H2B / DIHYDROBIOPTERIN / OXIDOREDUCTASE-TRANSFERASE complex | ||||||
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 / OTHER / Resolution: 2.35 Å | ||||||
Authors | Crane, B.R. / Arvai, A.S. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structures of the N(Omega)-Hydroxy-L-Arginine Complex of Inducible Nitric Oxide Synthase Oxygenase Dimer with Active Andinactive Pterins Authors: Crane, B.R. / Arvai, A.S. / Ghosh, S. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. #1: Journal: Embo J. / Year: 1999 Title: N-Terminal Domain Swapping and Metal Ion Binding in Nitric Oxide Synthase Dimerization Authors: Crane, B.R. / Rosenfeld, R.A. / Arvai, A.S. / Ghosh, D.K. / Ghosh, S. / Tainer, J.A. / Stuehr, D.J. / Getzoff, E.D. #2: Journal: Embo J. / Year: 1999 Title: Inducible Nitric Oxide Synthase: Role of the N-Terminal Beta-Hairpin Hook and Pterin-Binding Segment in Dimerization and Tetrahydrobiopterin Interaction Authors: Ghosh, D.K. / Crane, B.R. / Ghosh, S. / Wolan, D. / Gachhui, R. / Crooks, C. / Presta, A. / Tainer, J.A. / Getzoff, E.D. / Stuehr, D.J. #3: Journal: Science / Year: 1998 Title: Structure of Nitric Oxide Synthase Oxygenase Dimer with Pterin and Substrate Authors: Crane, B.R. / Arvai, A.S. / Ghosh, D.K. / Wu, C. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. #4: Journal: Science / Year: 1997 Title: The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complexes Authors: Crane, B.R. / Arvai, A.S. / Gachhui, R. / Wu, C. / Ghosh, D.K. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: KABSCH AND SANDER |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dww.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dww.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 1dww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dww_validation.pdf.gz | 603 KB | Display | wwPDB validaton report |
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Full document | 1dww_full_validation.pdf.gz | 621.9 KB | Display | |
Data in XML | 1dww_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 1dww_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/1dww ftp://data.pdbj.org/pub/pdb/validation_reports/dw/1dww | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | BIOLOGICAL_UNIT: INOS OXYGENASE DOMAIN ACTIVE AS A DIMER |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48626.297 Da / Num. of mol.: 2 / Fragment: OXYGENASE DOMAIN 65-498 Source method: isolated from a genetically manipulated source Details: MURINE INDUCIBLE / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell: MACROPHAGE / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29477, nitric-oxide synthase (NADPH) |
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-Non-polymers , 6 types, 707 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | EACH NOS DIMER IS COVALENTLY LINKED BY A TETRATHIOLATE ZINC CENTER THAT RESIDES ON THE MOLECULAR ...EACH NOS DIMER IS COVALENTLY |
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Sequence details | PROTEIN WAS EXPRESSED WITH A COOH-TERMINAL HIS6 TAG. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. obs: 62465 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 46.9 Å2 / Rsym value: 0.074 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 2.35→2.43 Å / Mean I/σ(I) obs: 7.4 / Rsym value: 0.289 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 303449 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.289 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.35→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3681934.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 52.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 2.1 Å2 / Rms dev position: 0.04 Å / Weight Biso : 0.95 / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'X-PLOR CNS 0.4' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.43 Å / Rfactor Rfree: 0.414 / Rfactor obs: 0.375 |