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Yorodumi- PDB-3jwu: Structure of rat neuronal nitric oxide synthase R349A mutant heme... -
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-Basic information
Entry | Database: PDB / ID: 3jwu | ||||||
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Title | Structure of rat neuronal nitric oxide synthase R349A mutant heme domain in complex with N1-{(3'R,4'S)-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}-N2-(3'-fluorophenethyl)ethane-1,2-diamine tetrahydrochloride | ||||||
Components | Nitric oxide synthase, brain | ||||||
Keywords | OXIDOREDUCTASE / heme enzyme / substrate inhibitor | ||||||
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: 1.93 Å | ||||||
Authors | Delker, S.L. / Li, H. / Poulos, T.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Unexpected binding modes of nitric oxide synthase inhibitors effective in the prevention of a cerebral palsy phenotype in an animal model. Authors: Delker, S.L. / Ji, H. / Li, H. / Jamal, J. / Fang, J. / Xue, F. / Silverman, R.B. / 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 | 3jwu.cif.gz | 313.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jwu.ent.gz | 244.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jwu_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3jwu_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3jwu_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 3jwu_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/3jwu ftp://data.pdbj.org/pub/pdb/validation_reports/jw/3jwu | HTTPS FTP |
-Related structure data
Related structure data | 3jwsC 3jwtC 3jwvC 3jwwC 3jwxC 3jwyC 3jwzC 3jx0C 3jx1C 3jx2C 3jx3C 3jx4C 3jx5C 3jx6C 1om4S 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: 48726.410 Da / Num. of mol.: 2 / Fragment: Residues 297-718 / Mutation: R349A 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 , 6 types, 400 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ZN / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.61 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / 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: BL9-2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 21, 2007 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 71872 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 34.82 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 4 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2 / Rsym value: 0.648 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1OM4 Resolution: 1.93→38.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.506 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.132 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.149 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.93→38.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.97 Å / Total num. of bins used: 20
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Refinement TLS params. | T33: 0.0757 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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