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Yorodumi- PDB-3hso: Ternary structure of neuronal nitric oxide synthase with NHA and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hso | ||||||
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Title | Ternary structure of neuronal nitric oxide synthase with NHA and NO bound(1) | ||||||
Components | Nitric oxide synthase, brain | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase heme enzyme diatomic ligand / Alternative splicing / Calmodulin-binding / Cell membrane / Cell projection / FAD / FMN / Heme / Iron / Membrane / Metal-binding / NADP | ||||||
Function / homology | Function and homology information Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport / response to nitric oxide / nitric oxide metabolic process / postsynaptic specialization, intracellular component / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Ion homeostasis / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / negative regulation of calcium ion transport / calyx of Held / behavioral response to cocaine / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase (NADPH) / sodium channel regulator activity / response to vitamin E / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / negative regulation of insulin secretion / nitric oxide mediated signal transduction / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / arginine catabolic process / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / sarcoplasmic reticulum membrane / T-tubule / cellular response to epinephrine stimulus / : / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to nutrient levels / potassium ion transport / response to hormone / sarcoplasmic reticulum / secretory granule / response to activity / positive regulation of long-term synaptic potentiation / establishment of localization in cell / cell periphery / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / establishment of protein localization / cellular response to mechanical stimulus / vasodilation / response to organic cyclic compound / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / response to estrogen / calcium-dependent protein binding / calcium ion transport / positive regulation of peptidyl-serine phosphorylation / FMN binding / ATPase binding / NADP binding / flavin adenine dinucleotide binding / nuclear membrane / response to heat / scaffold protein binding / response to ethanol / negative regulation of neuron apoptotic process / transmembrane transporter binding / mitochondrial outer membrane / response to lipopolysaccharide / dendritic spine / calmodulin binding / postsynaptic density / cytoskeleton / response to hypoxia / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / synapse / dendrite / heme binding / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.02 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 | 3hso.cif.gz | 365.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hso.ent.gz | 296.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hso_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3hso_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3hso_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 3hso_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/3hso ftp://data.pdbj.org/pub/pdb/validation_reports/hs/3hso | HTTPS FTP |
-Related structure data
Related structure data | 3hsnC 3hspC 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 , 7 types, 452 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ZN / | #8: 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: 49.03 % |
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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: BL1-5 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2006 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 59511 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.02→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.256 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB CODE 1LZX Resolution: 2.02→49.15 Å / SU ML: 0.29 / 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: 61.22 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→49.15 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 |