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- PDB-2nod: MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER (DELTA 65)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nod | ||||||
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Title | MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER (DELTA 65) WITH TETRAHYDROBIOPTERIN AND WATER BOUND IN ACTIVE CENTER | ||||||
![]() | NITRIC OXIDE SYNTHASE | ||||||
![]() | OXIDOREDUCTASE / NITRIC OXIDE L-ARGININE MONOOXYGENASE / HEME / DIMER / NOS | ||||||
Function / homology | ![]() Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / peptidyl-cysteine S-nitrosylation / Peroxisomal protein import / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / superoxide metabolic process / cortical cytoskeleton / regulation of cytokine production involved in inflammatory response ...Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / peptidyl-cysteine S-nitrosylation / Peroxisomal protein import / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / superoxide metabolic process / cortical cytoskeleton / regulation of cytokine production involved in inflammatory response / cellular response to cytokine stimulus / Fc-gamma receptor signaling pathway involved in phagocytosis / : / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / nitric oxide biosynthetic process / regulation of insulin secretion / positive regulation of interleukin-8 production / response to bacterium / negative regulation of protein catabolic process / cellular response to type II interferon / positive regulation of interleukin-6 production / circadian rhythm / peroxisome / FMN binding / cellular response to xenobiotic stimulus / flavin adenine dinucleotide binding / NADP binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / response to hypoxia / calmodulin binding / defense response to bacterium / inflammatory response / negative regulation of gene expression / heme binding / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Crane, B.R. / Arvai, A.S. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. | ||||||
![]() | ![]() 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. #1: ![]() 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. #2: ![]() Title: Characterization of the Inducible Nitric Oxide Synthase Oxygenase Domain Identifies a 49 Amino Acid Segment Required for Subunit Dimerization and Tetrahydrobiopterin Interaction Authors: Ghosh, D.K. / Wu, C. / Pitters, E. / Moloney, M. / Werner, E.R. / Mayer, B. / Stuehr, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192 KB | Display | ![]() |
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PDB format | ![]() | 150.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1nodSC ![]() 3nodC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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: (Code: given Matrix: (-0.864913, -0.501901, -0.004529), Vector: |
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Components
#1: Protein | Mass: 48998.691 Da / Num. of mol.: 2 / Fragment: OXYGENASE DOMAIN 65-498 Source method: isolated from a genetically manipulated source Details: MURINE INDUCIBLE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 42826 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 53.1 Å2 / Rsym value: 0.056 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.25 / % possible all: 66.4 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 66.4 % / Rmerge(I) obs: 0.25 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NOD Resolution: 2.6→20 Å / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: PRONOUNCED ANISOTROPIC DIFFRACTION COMPLICATED INDIVIDUAL B-FACTOR REFINEMENT. INDIVIDUAL B-FACTORS WERE REFINED TO MINIMIZE R-FREE AND PRODUCE AN AVERAGE COMMENSURATE WITH WILSON SCALING.
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Displacement parameters | Biso mean: 49.9 Å2
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Refine analyze | Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: 71% OF BACKBONE / Rms dev Biso : 2 Å2 / Rms dev position: 100 Å / Weight Biso : 0 / Weight position: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.7 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.348 |