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Yorodumi- 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 | ||||||
Components | Superoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / MNSOD / MANGANESE SUPEROXIDE DISMUTASE / Y34N 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 / 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 / glutathione metabolic process / respiratory electron transport chain / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / release of cytochrome c from mitochondria / post-embryonic development / regulation of mitochondrial membrane potential / liver development / locomotory behavior / response to activity / response to gamma radiation / Transcriptional activation of mitochondrial biogenesis / response to hydrogen peroxide / 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 / heart development / manganese ion binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Perry, J.J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p4k.cif.gz | 343.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p4k.ent.gz | 278.1 KB | Display | PDB format |
PDBx/mmJSON format | 2p4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4k ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4k | HTTPS FTP |
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-Related structure data
Related structure data | 1zspC 1zteC 1zuqC 1n0jS 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
#1: Protein | Mass: 22184.041 Da / Num. of mol.: 4 / Mutation: Y34N 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: 2.19 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: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.03 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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