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Yorodumi- PDB-3hw7: High pressure (0.57 GPa) crystal structure of bovine copper, zinc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hw7 | ||||||
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Title | High pressure (0.57 GPa) crystal structure of bovine copper, zinc superoxide dismutase at 2.0 angstroms | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / METAL BINDING PROTEIN / BOVINE / SUPEROXIDE DISMUTASE / high pressure / flexible electrostatic loop / Antioxidant / Disulfide bond / Metal-binding | ||||||
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: 2 Å | ||||||
Authors | Ascone, I. / Savino, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa Authors: Ascone, I. / Savino, C. / Kahn, R. / Fourme, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hw7.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hw7.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/3hw7 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/3hw7 | HTTPS FTP |
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-Related structure data
Related structure data | 1cbjS 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 / Source: (natural) Bos taurus (cattle) / Cell: ERYTHROCYTES / References: UniProt: P00442, superoxide dismutase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CU / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID27 / Wavelength: 0.331 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 29, 2005 |
Radiation | Monochromator: Si(111)monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.331 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.9 Å / Num. obs: 22012 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2893 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBJ Resolution: 2→19.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.439 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.211 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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