+Open data
-Basic information
Entry | Database: PDB / ID: 2z7y | ||||||
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Title | Crystal Structure of H2O2 treated Cu,Zn-SOD | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / metalloprotein / dismutase / hydrogen peroxide / Acetylation / Antioxidant / Copper / Cytoplasm / Metal-binding / Zinc | ||||||
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 / superoxide dismutase / positive regulation of catalytic activity / 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 / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Ito, S. / Ishii, T. / Uchida, K. | ||||||
Citation | Journal: To be Published Title: Crystal structure of H2O2-treated Cu,Zn-superoxide dismutase Authors: Ito, S. / Ishii, T. / Uchida, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z7y.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z7y.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 2z7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/2z7y ftp://data.pdbj.org/pub/pdb/validation_reports/z7/2z7y | HTTPS FTP |
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-Related structure data
Related structure data | 2z7zC 1e9qS 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: 15573.337 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: sigma-aldrich chemical company / Source: (natural) Bos taurus (cattle) / Cell: erythrocyte / References: UniProt: P00442, superoxide dismutase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | REDOX STATE OF COPPER IONS OF OUR ENTRIES ARE AMBIGUOUS. ESPECIALLY, COPPER BOND OXIDANT, DESCRIBED ...REDOX STATE OF COPPER IONS OF OUR ENTRIES ARE AMBIGUOUS. ESPECIALLY | |
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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: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→28.1 Å / Num. all: 51639 / Num. obs: 51639 / Biso Wilson estimate: 20 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E9Q Resolution: 1.55→28.1 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1451994.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.0318 Å2 / ksol: 0.35397 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→28.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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