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Yorodumi- PDB-2gds: Interrupting the Hydrogen Bonding Network at the Active Site of H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gds | ||||||
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Title | Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase | ||||||
Components | Superoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / Human Manganese Superoxide Dismutase / H30N mutation | ||||||
Function / homology | Function and homology information acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / cellular response to ethanol / superoxide anion generation / hydrogen peroxide biosynthetic process / response to manganese ion / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of fat cell differentiation / response to zinc ion / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / response to immobilization stress / response to axon injury / neuron development / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / glutathione metabolic process / response to electrical stimulus / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / respiratory electron transport chain / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / post-embryonic development / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / liver development / response to activity / locomotory behavior / response to gamma radiation / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / oxygen binding / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / positive regulation of nitric oxide biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to oxidative stress / manganese ion binding / heart development / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / mitochondrial matrix / positive regulation of cell migration / response to xenobiotic stimulus / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Perry, J.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Interrupting the Hydrogen Bond Network at the Active Site of Human Manganese Superoxide Dismutase Authors: Ramilo, C.A. / Leveque, V. / Guan, Y. / Lepock, J.R. / Tainer, J.A. / Nick, H.S. / Silverman, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gds.cif.gz | 181.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gds.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 2gds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/2gds ftp://data.pdbj.org/pub/pdb/validation_reports/gd/2gds | HTTPS FTP |
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-Related structure data
Related structure data | 1qnmS 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 | The Biological assembly is a tetramer |
-Components
#1: Protein | Mass: 22209.068 Da / Num. of mol.: 4 / Mutation: H30N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD2 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): QC774I (SOD--) / References: UniProt: P04179, superoxide dismutase #2: Chemical | ChemComp-MN / #3: 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: 2.18 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.8 Details: 19.3mg/ml protein, 25mM potassium phosphate, 20% polyethylene glycol 2000, monomethyl ether, pH 7.80, VAPOR DIFFUSION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Sep 29, 1998 / Details: FLAT MIRROR (VERTICAL FOCUSING) |
Radiation | Monochromator: SINGLE CRYSTAL Si(311) BENT MON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. obs: 35154 / Biso Wilson estimate: 26 Å2 / Rsym value: 0.064 |
Reflection shell | Highest resolution: 2.3 Å / Rsym value: 0.364 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QNM Highest resolution: 2.3 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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