+Open data
-Basic information
Entry | Database: PDB / ID: 1e9o | ||||||
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Title | Crystal structure of bovine SOD - 1 of 3 | ||||||
Components | (SUPEROXIDE DISMUTASE) x 2 | ||||||
Keywords | OXIDOREDUCTASE / SOD / ENZYME / SUPEROXIDE / ASYMMETRY | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Hough, M.A. / Samar Hasnain, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Conformational Variability of the Cu Site in One Subunit of Bovine Cuzn Superoxide Dismutase: The Importance of Mobility in the Glu119-Leu142 Loop Region for Catalytic Function Authors: Hough, M.A. / Strange, R.W. / 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 | 1e9o.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e9o.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 1e9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/1e9o ftp://data.pdbj.org/pub/pdb/validation_reports/e9/1e9o | HTTPS FTP |
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-Related structure data
Related structure data | 1e9pC 1e9qC 1cbjS 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: 15578.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Cell: EUKARYOTE / Cellular location: CYTOPLASM / Organ: BLOOD / References: UniProt: P00442, superoxide dismutase | ||||
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#2: Protein | Mass: 15648.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Cell: EUKARYOTE / Cellular location: CYTOPLASM / Organ: BLOOD / References: UniProt: P00442, superoxide dismutase | ||||
#3: Chemical | ChemComp-CU / #4: Water | ChemComp-HOH / | Compound details | DESTROYS RADICALS TOXIC TO BIOLOGICAL SYSTEMS WHICH ARE NORMALLY PRODUCED WITHIN THE CELLS 2 ...DESTROYS RADICALS TOXIC TO BIOLOGICAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 55 % | ||||||||||||||||||
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Crystal grow | pH: 4 / Details: PEG-4000, NACL, pH 4.00 | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25 Å / Num. obs: 68261 / % possible obs: 83.7 % / Redundancy: 3 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / % possible all: 84 |
Reflection | *PLUS Num. obs: 25532 / Num. measured all: 68261 |
Reflection shell | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBJ Resolution: 1.85→8 Å / SU B: 2.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15
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Displacement parameters | Biso mean: 24.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |