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- PDB-1m00: Rat neuronal NOS heme domain with N-butyl-N'-hydroxyguanidine bound -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m00 | ||||||
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Title | Rat neuronal NOS heme domain with N-butyl-N'-hydroxyguanidine bound | ||||||
![]() | Nitric-oxide synthase | ||||||
![]() | OXIDOREDUCTASE / nitric oxide synthase / oxydoreductase / heme-enzyme | ||||||
Function / homology | ![]() Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / 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 / 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 / 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 / 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 / calyx of Held / negative regulation of potassium ion transport / behavioral response to cocaine / negative regulation of calcium ion transport / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase (NADPH) / response to vitamin E / sodium channel regulator activity / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / negative regulation of insulin secretion / nitric oxide mediated signal transduction / multicellular organismal response to stress / nitric-oxide synthase activity / xenobiotic catabolic process / NADPH binding / arginine catabolic process / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / T-tubule / : / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to nutrient levels / response to hormone / secretory granule / response to activity / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / muscle contraction / establishment of localization in cell / cell periphery / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / potassium ion transport / establishment of protein localization / response to organic cyclic compound / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / cellular response to mechanical stimulus / response to estrogen / vasodilation / calcium ion transport / calcium-dependent protein binding / FMN binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / flavin adenine dinucleotide binding / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / negative regulation of neuron apoptotic process / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / calmodulin binding / response to hypoxia / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / synapse / dendrite / heme binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.6 KB | Display | ![]() |
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PDB format | ![]() | 151 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 39.3 KB | Display | |
Data in CIF | ![]() | 55.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 507 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/BHH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/BHH.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 % |
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Processing
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Refinement | Method to determine structure: ![]() 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 |