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Yorodumi- PDB-1sda: CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXI... -
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-Basic information
Entry | Database: PDB / ID: 1sda | ||||||
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Title | CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE | ||||||
Components | COPPER,ZINC SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE(COPPER) | ||||||
Function / homology | Function and homology information Platelet degranulation / Detoxification of Reactive Oxygen Species / 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 / auditory receptor cell stereocilium organization ...Platelet degranulation / Detoxification of Reactive Oxygen Species / 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 / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / regulation of protein kinase activity / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / heart contraction / superoxide metabolic process / superoxide dismutase / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / embryo implantation / dendrite cytoplasm / reactive oxygen species metabolic process / removal of superoxide radicals / glutathione metabolic process / : / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / sensory perception of sound / response to hydrogen peroxide / regulation of blood pressure / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / protein-folding chaperone binding / response to heat / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Smith, C.D. / Carson, M. / Van Der Woerd, M. / Chen, J. / Ischiropoulos, H. / Beckman, J.S. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 1992 Title: Crystal structure of peroxynitrite-modified bovine Cu,Zn superoxide dismutase. Authors: Smith, C.D. / Carson, M. / van der Woerd, M. / Chen, J. / Ischiropoulos, H. / Beckman, J.S. #1: Journal: Arch.Biochem.Biophys. / Year: 1992 Title: Peroxynitrite-Mediated Tyrosine Nitration Catalyzed by Superoxide Dismutase Authors: Ischiropoulos, H. / Zhu, L. / Chen, J. / Tsai, M. / Martin, J.C. / Smith, C.D. / Beckman, J.S. #2: Journal: J.Mol.Biol. / Year: 1982 Title: Determination and Analysis of the 2 Angstroms Structure of Copper, Zinc Superoxide Dismutase Authors: Tainer, J.A. / Getzoff, E.D. / Beem, K.M. / Richardson, J.S. / Richardson, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sda.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sda.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 1sda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sda_validation.pdf.gz | 390.6 KB | Display | wwPDB validaton report |
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Full document | 1sda_full_validation.pdf.gz | 401.9 KB | Display | |
Data in XML | 1sda_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1sda_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/1sda ftp://data.pdbj.org/pub/pdb/validation_reports/sd/1sda | HTTPS FTP |
-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: 15644.371 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 / | Compound details | EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION AND A ...EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION AND A WATER MOLECULE. THE DOMINANT STRUCTURAL | |
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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 Temperature: 5 ℃ / pH: 7.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Rmerge(I) obs: 0.323 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.187 / Rfactor obs: 0.187 / Highest resolution: 2.5 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). FOR THE ACTIVE SITE HISTIDINES, THE PLACEMENT OF HYDROGENS WAS AS FOLLOWS FOR X-PLOR REFINEMENT: HIS 46, 118 HAVE A HYDROGEN ON THE DELTA NITROGEN; HIS 44, 69, 78 HAVE A HYDROGEN ON THE EPSILON NITROGEN; AND HIS 61 IS NEGATIVELY CHARGED WITH NEITHER HYDROGEN. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / Rfactor obs: 0.187 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.23 |