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- PDB-2p4k: Contribution to Structure and Catalysis of Tyrosine 34 in Human M... -
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Basic information
Entry | Database: PDB / ID: 2p4k | ||||||
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Title | Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase | ||||||
![]() | Superoxide dismutase | ||||||
![]() | OXIDOREDUCTASE / MNSOD / MANGANESE SUPEROXIDE DISMUTASE / Y34N MUTATION | ||||||
Function / homology | ![]() 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 / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / negative regulation of fat cell differentiation / response to zinc ion / 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 / response to electrical stimulus / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / respiratory electron transport chain / glutathione metabolic process / release of cytochrome c from mitochondria / post-embryonic development / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / heart development / manganese ion binding / cellular response to oxidative stress / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perry, J.J. | ||||||
![]() | ![]() Title: Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. Authors: Perry, J.J. / Hearn, A.S. / Cabelli, D.E. / Nick, H.S. / Tainer, J.A. / Silverman, D.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.8 KB | Display | ![]() |
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PDB format | ![]() | 278.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447 KB | Display | ![]() |
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Full document | ![]() | 451.4 KB | Display | |
Data in XML | ![]() | 42.9 KB | Display | |
Data in CIF | ![]() | 65.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zspC ![]() 1zteC ![]() 1zuqC ![]() 1n0jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22184.041 Da / Num. of mol.: 4 / Mutation: Y34N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 25 MM K2HPO4, 22% POLYETHYLENE GLYCOL (PEG) 2000 MONOMETHYL ETHER, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 2, 2003 |
Radiation | Monochromator: SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→39.2 Å / Num. all: 128773 / Num. obs: 115223 / % possible obs: 96.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.48→1.57 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 5 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N0J Resolution: 1.48→39.2 Å / Num. parameters: 61276 / Num. restraintsaints: 73318 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7482 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→39.2 Å
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Refine LS restraints |
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