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Yorodumi- PDB-4fvy: Structure of rat nNOS heme domain in complex with N(omega)-hydrox... -
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-Basic information
Entry | Database: PDB / ID: 4fvy | ||||||
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Title | Structure of rat nNOS heme domain in complex with N(omega)-hydroxy- N(omega)-methyl-L-arginine | ||||||
Components | Nitric oxide synthase, brain | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase / substrate analog | ||||||
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 / Ion homeostasis / nitric oxide metabolic process / postsynaptic specialization, intracellular component / response to nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / calyx of Held / negative regulation of calcium ion transport / behavioral response to cocaine / regulation of neurogenesis / negative regulation of serotonin uptake / response to vitamin E / nitric-oxide synthase (NADPH) / sodium channel regulator activity / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / nitric oxide mediated signal transduction / negative regulation of insulin secretion / nitric-oxide synthase activity / xenobiotic catabolic process / multicellular organismal response to stress / arginine catabolic process / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / sarcoplasmic reticulum membrane / T-tubule / nitric oxide biosynthetic process / cellular response to epinephrine stimulus / negative regulation of blood pressure / photoreceptor inner segment / response to hormone / response to nutrient levels / sarcoplasmic reticulum / secretory granule / response to activity / positive regulation of long-term synaptic potentiation / cell periphery / establishment of localization in cell / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / establishment of protein localization / potassium ion transport / caveola / 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-dependent protein binding / calcium ion transport / 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 / negative regulation of neuron apoptotic process / transmembrane transporter binding / mitochondrial outer membrane / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / response to hypoxia / calmodulin binding / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / dendrite / heme binding / synapse / 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: 1.7 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Methylated N(omega)-Hydroxy-l-arginine Analogues as Mechanistic Probes for the Second Step of the Nitric Oxide Synthase-Catalyzed Reaction Authors: Jansen Labby, K. / Li, H. / Roman, L.J. / Martasek, P. / Poulos, T.L. / Silverman, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fvy.cif.gz | 359.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fvy.ent.gz | 291.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fvy_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4fvy_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4fvy_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 4fvy_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/4fvy ftp://data.pdbj.org/pub/pdb/validation_reports/fv/4fvy | HTTPS FTP |
-Related structure data
Related structure data | 4fvwC 4fvxC 4fvzC 4fw0C 4gqeC 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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Details | subunit A / subunit B / prosthetic group / cofactor / substrate analog / buffer component / metal center |
-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 , 6 types, 428 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 20-22% PEG3350, 0.1M Cacodylate, 140-200mM ammonium acetate, 10% ethylene glycol, 5mM GSH, 35uM SDS, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2009 / 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: 1.7→50 Å / Num. obs: 102661 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2 / Rsym value: 0.443 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1OM4 Resolution: 1.7→49.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.219 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / 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: 36.517 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→49.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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