[English] 日本語
Yorodumi- PDB-2nod: MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER (DELTA 65)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nod | ||||||
---|---|---|---|---|---|---|---|
Title | MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER (DELTA 65) WITH TETRAHYDROBIOPTERIN AND WATER BOUND IN ACTIVE CENTER | ||||||
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 / prostaglandin secretion / positive regulation of killing of cells of another organism / 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 / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton / superoxide metabolic process / cGMP-mediated signaling / nitric-oxide synthase binding / cellular response to cytokine stimulus / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / regulation of insulin secretion / cellular response to organic cyclic compound / nitric-oxide synthase (NADPH) / blood vessel remodeling / response to tumor necrosis factor / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / positive regulation of interleukin-8 production / response to bacterium / Hsp90 protein binding / negative regulation of protein catabolic process / beta-catenin binding / regulation of blood pressure / peroxisome / positive regulation of interleukin-6 production / cellular response to type II interferon / circadian rhythm / cellular response to xenobiotic stimulus / FMN binding / flavin adenine dinucleotide binding / NADP binding / actin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / response to hypoxia / calmodulin binding / 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 / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Crane, B.R. / Arvai, A.S. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. | ||||||
Citation | 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. #1: 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. #2: Journal: Biochemistry / Year: 1997 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2nod.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2nod.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 2nod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/2nod ftp://data.pdbj.org/pub/pdb/validation_reports/no/2nod | HTTPS FTP |
---|
-Related structure data
Related structure data | 1nodSC 3nodC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.864913, -0.501901, -0.004529), Vector: |
-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.) Mus musculus (house mouse) / Cell: MACROPHAGE / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / References: UniProt: P29477, nitric-oxide synthase (NADPH) #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.348 |