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Yorodumi- PDB-3hsp: Ternary structure of neuronal nitric oxide synthase with NHA and ... -
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-Basic information
Entry | Database: PDB / ID: 3hsp | ||||||
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Title | Ternary structure of neuronal nitric oxide synthase with NHA and NO bound(2) | ||||||
Components | Nitric oxide synthase, brain | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase heme enzyme diatomic ligand / Calmodulin-binding / Cell membrane / Cell projection / FAD / FMN / Heme / Iron / Membrane / Metal-binding / NADP | ||||||
Function / homology | Function and homology information positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis ...positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis / positive regulation of sodium ion transmembrane transport / response to nitric oxide / postsynaptic specialization, intracellular component / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / behavioral response to cocaine / postsynaptic density, intracellular component / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / calyx of Held / negative regulation of calcium ion transport / negative regulation of serotonin uptake / sodium channel regulator activity / regulation of neurogenesis / striated muscle contraction / regulation of postsynaptic membrane potential / negative regulation of insulin secretion / response to vitamin E / nitric-oxide synthase (NADPH) / multicellular organismal response to stress / xenobiotic catabolic process / nitric-oxide synthase activity / negative regulation of peptidyl-serine phosphorylation / nitric oxide mediated signal transduction / arginine catabolic process / NADPH binding / regulation of sodium ion transport / response to organonitrogen compound / cellular response to epinephrine stimulus / sarcoplasmic reticulum membrane / T-tubule / photoreceptor inner segment / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / response to nutrient levels / response to activity / response to nicotine / sarcoplasmic reticulum / muscle contraction / secretory granule / female pregnancy / positive regulation of long-term synaptic potentiation / cell periphery / establishment of localization in cell / phosphoprotein binding / response to lead ion / sarcolemma / establishment of protein localization / potassium ion transport / response to organic cyclic compound / response to peptide hormone / cellular response to growth factor stimulus / Z disc / vasodilation / cellular response to mechanical stimulus / response to estrogen / calcium-dependent protein binding / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / ATPase binding / response to heat / scaffold protein binding / response to ethanol / nuclear membrane / negative regulation of neuron apoptotic process / mitochondrial outer membrane / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia / cytoskeleton / calmodulin binding / membrane raft / negative regulation of cell population proliferation / dendrite / glutamatergic synapse / synapse / heme binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Doukov, T. / Li, H. / Soltis, M. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Single crystal structural and absorption spectral characterizations of nitric oxide synthase complexed with N(omega)-hydroxy-L-arginine and diatomic ligands. Authors: Doukov, T. / Li, H. / Soltis, M. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hsp.cif.gz | 364.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hsp.ent.gz | 295.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/3hsp ftp://data.pdbj.org/pub/pdb/validation_reports/hs/3hsp | HTTPS FTP |
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-Related structure data
Related structure data | 3hsnC 3hsoC 1lzxS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48812.527 Da / Num. of mol.: 2 / Fragment: UNP residues 297-718 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nos1, Bnos / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH) |
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-Non-polymers , 8 types, 407 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ZN / | #8: Chemical | ChemComp-GOL / #9: 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: 2.41 Å3/Da / Density % sol: 49.04 % |
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Crystal grow | Temperature: 278 K / pH: 5.8 Details: PEG3350, MES, ammonium acetate SDS, GSH, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.978 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 48552 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.505 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB CODE 1LZX Resolution: 2.2→19.82 Å / SU ML: 0.28 / Isotropic thermal model: isotropic / σ(F): 1.99 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.31 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.82 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: CHAIN B |