+Open data
-Basic information
Entry | Database: PDB / ID: 1cbj | ||||||
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Title | CRYSTAL STRUCTURE OF BOVINE SUPEROXIDE DISMUTASE CRYSTAL. | ||||||
Components | PROTEIN (SUPEROXIDE DISMUTASE) | ||||||
Keywords | OXIDOREDUCTASE / CUZN SUPEROXIDE DISMUTASE / FUNCTIONAL ASYMMETRY / DISORDER | ||||||
Function / homology | Function and homology information neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / 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 / removal of superoxide radicals / glutathione metabolic process / ovarian follicle development / embryo implantation / reactive oxygen species metabolic process / dendrite cytoplasm / regulation of mitochondrial membrane potential / locomotory behavior / 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 / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Hough, M.A. / Hasnain, S.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystallographic structures of bovine copper-zinc superoxide dismutase reveal asymmetry in two subunits: functionally important three and five coordinate copper sites captured in the same crystal. Authors: Hough, M.A. / Hasnain, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cbj.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cbj.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 1cbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/1cbj ftp://data.pdbj.org/pub/pdb/validation_reports/cb/1cbj | HTTPS FTP |
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-Related structure data
Related structure data | 1cb4C 1cobS S: Starting model for refinement C: citing same article (ref.) |
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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: 15573.337 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ONE COPPER(II) SITE, ONE CU(I) SITE. / Source: (natural) Bos taurus (cattle) / Cell: ERYTHROCYTES / References: UniProt: P00442, superoxide dismutase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | REDUCED COPPER OXIDIZED COPPER ZINC SITE ZINC SITE SUBUNIT A CONTAINS A THREE COORDINATE, CU(I) ...REDUCED COPPER OXIDIZED COPPER ZINC SITE ZINC SITE SUBUNIT A CONTAINS A THREE COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 55 % | ||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 55 % | ||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 4, 1997 / Details: MIRRORS |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→15 Å / Num. obs: 39196 / % possible obs: 89.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.6 / % possible all: 68.2 |
Reflection | *PLUS % possible obs: 89.1 % / Num. measured all: 172498 |
Reflection shell | *PLUS % possible obs: 68.2 % / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1COB Resolution: 1.65→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: XPLOR SIMULATED ANNEALING ALSO USED
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Displacement parameters | Biso mean: 23.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.65 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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