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Yorodumi- PDB-1m00: Rat neuronal NOS heme domain with N-butyl-N'-hydroxyguanidine bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m00 | ||||||
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Title | Rat neuronal NOS heme domain with N-butyl-N'-hydroxyguanidine bound | ||||||
Components | Nitric-oxide synthaseNitric oxide synthase | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase / oxydoreductase / heme-enzyme | ||||||
Function / homology | Function and homology information 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 ...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 / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / response to nitric oxide / postsynaptic specialization, intracellular component / nitric oxide metabolic process / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / postsynaptic density, intracellular component / cadmium ion binding / behavioral response to cocaine / 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 / negative regulation of insulin secretion / response to vitamin E / nitric-oxide synthase (NADPH) / regulation of postsynaptic membrane potential / multicellular organismal response to stress / nitric-oxide synthase activity / xenobiotic catabolic process / arginine catabolic process / negative regulation of peptidyl-serine phosphorylation / NADPH binding / regulation of sodium ion transport / nitric oxide mediated signal transduction / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / T-tubule / response to organonitrogen compound / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / 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 / cellular response to mechanical stimulus / response to estrogen / vasodilation / 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 / synapse / glutamatergic 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 Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Li, H. / Shimizu, H. / Flinspach, M. / Jamal, J. / Yang, W. / Xian, M. / Cai, T. / Wen, E.Z. / Jia, Q. / Wang, P.G. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: The Novel Binding Mode of N-Alkyl-N'-Hydroxyguanidine to Neuronal Nitric Oxide Synthase Provides Mechanistic Insights into NO Biosynthesis Authors: Li, H. / Shimizu, H. / Flinspach, M. / Jamal, J. / Yang, W. / Xian, M. / Cai, T. / Wen, E.Z. / Jia, Q. / Wang, P.G. / Poulos, T.L. #1: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystal Structure of Constitutive Endothelial Nitric Oxide Synthase: a Paradigm for Pterin Function Involving a Novel Metal Center Authors: Raman, C.S. / Li, H. / Martasek, P. / Kral, V. / Masters, B.S. / 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 | 1m00.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m00.ent.gz | 151 KB | Display | PDB format |
PDBx/mmJSON format | 1m00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m00 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m00 | HTTPS FTP |
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-Related 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: 48555.215 Da / Num. of mol.: 2 / Fragment: heme domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: brain / Plasmid: pCWori / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH) |
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-Non-polymers , 6 types, 507 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.44 Å3/Da / Density % sol: 49.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG4000, MES, ammonium acetate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 280K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / PH range low: 6 / PH range high: 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
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: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 2001 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 58402 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2739 / Rsym value: 0.621 / % possible all: 90.7 |
Reflection | *PLUS Num. measured all: 173591 |
Reflection shell | *PLUS % possible obs: 90.7 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→49.03 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues 339-349 in subunit A and 339-347 in subunit B are disordered and therefore are not included in the model.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.9754 Å2 / ksol: 0.367686 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→49.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.35 |