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Yorodumi- PDB-2sod: DETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2sod | |||||||||
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Title | DETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE | |||||||||
Components | COPPER,ZINC SUPEROXIDE DISMUTASE | |||||||||
Keywords | OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR) | |||||||||
Function / homology | Function and homology information neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / glutathione metabolic process / ovarian follicle development / embryo implantation / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / locomotory behavior / regulation of mitochondrial membrane potential / response to organic substance / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / regulation of blood pressure / peroxisome / protein polyubiquitination / ubiquitin-protein transferase activity / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Tainer, J.A. / Getzoff, E.D. / Richardson, J.S. / Richardson, D.C. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1982 Title: Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. Authors: Tainer, J.A. / Getzoff, E.D. / Beem, K.M. / Richardson, J.S. / Richardson, D.C. #1: Journal: Nature / Year: 1983 Title: Structure and Mechanism of Copper, Zinc Superoxide Dismutase Authors: Tainer, J.A. / Getzoff, E.D. / Richardson, J.S. / Richardson, D.C. #2: Journal: Nature / Year: 1983 Title: Electrostatic Recognition between Superoxide and Copper, Zinc Superoxide Dismutase Authors: Getzoff, E.D. / Tainer, J.A. / Weiner, P.K. / Kollman, P.A. / Richardson, J.S. / Richardson, D.C. #3: Journal: Biochemistry / Year: 1977 Title: Metal Sites of Copper-Zinc Superoxide Dismutase Authors: Beem, K.M. / Richardson, D.C. / Rajagopalan, K.V. #4: Journal: J.Mol.Biol. / Year: 1976 Title: Similarity of Three-Dimensional Structure between the Immunoglobulin Domain and the Copper,Zinc Superoxide Dismutase Subunit Authors: Richardson, J.S. / Richardson, D.C. / Thomas, K.A. / Silverton, E.W. / Davies, D.R. #5: Journal: Biochem.Biophys.Res.Commun. / Year: 1975 Title: Alpha-Carbon Coordinates for Bovine Cu,Zn Superoxide Dismutase Authors: Richardson, J.S. / Thomas, R.A. / Richardson, D.C. #6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975 Title: Crystal Structure of Bovine Cu,Zn Superoxide Dismutase at 3 Angstroms Resolution,Chain Tracing and Metal Ligands Authors: Richardson, J.S. / Thomas, K.A. / Rubin, B.H. / Richardson, D.C. #7: Journal: J.Biol.Chem. / Year: 1974 Title: The Crystal Structure of Bovine Cu2+,Zn2+ Superoxide Dismutase at 5.5 Angstroms Resolution Authors: Thomas, K.A. / Rubin, B.H. / Bier, C.J. / Richardson, J.S. / Richardson, D.C. #8: Journal: J.Biol.Chem. / Year: 1972 Title: Two Crystal Forms of Bovine Superoxide Dismutase Authors: Richardson, D.C. / Bier, C.J. / Richardson, J.S. | |||||||||
History |
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Remark 700 | SHEET EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION ...SHEET EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION AND A WATER MOLECULE. THE DOMINANT STRUCTURAL FEATURE OF EACH MONOMER IS AN EIGHT-STRANDED ANTI-PARALLEL BETA-BARREL. THERE ARE, HOWEVER, NO HYDROGEN BONDS BETWEEN STRANDS 4 AND 5. THIS BARREL IS DESCRIBED IN SHEET RECORDS BELOW AS A NINE-STRANDED SHEET WITH IDENTICAL FIRST AND LAST STRANDS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2sod.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2sod.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 2sod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/2sod ftp://data.pdbj.org/pub/pdb/validation_reports/so/2sod | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATION WHICH WILL PLACE THE YELLOW MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 1 BELOW. THE TRANSFORMATION WHICH WILL PLACE THE BLUE MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 2 BELOW. THE TRANSFORMATION WHICH WILL PLACE THE GREEN MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 3 BELOW. |
-Components
#1: Protein | Mass: 15599.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00442, superoxide dismutase #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.13 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 4 Å / Num. obs: 17206 / % possible obs: 35 % |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.256 / Highest resolution: 2 Å Details: COORDINATES IN THE A*BC ORTHOGONAL FRAME ARE PRESENTED BELOW FOR FOUR MONOMERS. ONE ENZYMATICALLY ACTIVE SOD DIMER COMPRISES MONOMERS ORANGE (CHAIN INDICATOR O) AND YELLOW (Y). ANOTHER DIMER ...Details: COORDINATES IN THE A*BC ORTHOGONAL FRAME ARE PRESENTED BELOW FOR FOUR MONOMERS. ONE ENZYMATICALLY ACTIVE SOD DIMER COMPRISES MONOMERS ORANGE (CHAIN INDICATOR O) AND YELLOW (Y). ANOTHER DIMER COMPRISES MONOMERS BLUE (B) AND GREEN (G). ONLY THOSE HYDROGEN BONDS OF WHICH THE DEPOSITORS ARE MOST CERTAIN ARE PRESENTED ON THE CONECT RECORDS BELOW. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 4 Å / Highest resolution: 2 Å / Rfactor obs: 0.255 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: o_bond_d / Dev ideal: 0.03 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS |