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Yorodumi- PDB-1n0j: The Structure of Human Mitochondrial MN3+ Superoxide Dismutase Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n0j | |||||||||
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Title | The Structure of Human Mitochondrial MN3+ Superoxide Dismutase Reveals a Novel Tetrameric Interface of Two 4-Helix Bundles | |||||||||
Components | Superoxide dismutase [Mn] | |||||||||
Keywords | OXIDOREDUCTASE / four-helix bundle / metalloenzyme / manganese | |||||||||
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 / superoxide anion generation / cellular response to ethanol / hydrogen peroxide biosynthetic process / response to manganese ion / negative regulation of fat cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to oxidative stress / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / response to zinc ion / 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 / neuron development / response to axon injury / 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 / locomotory behavior / regulation of mitochondrial membrane potential / liver development / response to activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Borgstahl, G.E.O. / Parge, H.E. / Tainer, J.A. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1992 Title: The Structure of Human Mitochondrial Mn3+ Superoxide Dismutase Reveals a Novel Tetrameric Interface of Two 4-Helix Bundles Authors: Borgstahl, G.E. / Parge, H.E. / Hickey, M.J. / Beyer Jr., W.F. / Hallewell, R.A. / Tainer, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n0j.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n0j.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/1n0j ftp://data.pdbj.org/pub/pdb/validation_reports/n0/1n0j | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8861, -0.4635, 0.0067), Vector: |
-Components
#1: Protein | Mass: 22364.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): SODASODB / References: UniProt: P04179, superoxide dismutase #2: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.81 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: peg 600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 47 % | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 19738 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 52 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 92 % / Num. measured all: 117362 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 52 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→10 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.171 / Rfactor Rwork: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |