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- PDB-2aeo: Crystal structure of cisplatinated bovine Cu,Zn superoxide dismutase -
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Open data
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Basic information
Entry | Database: PDB / ID: 2aeo | ||||||
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Title | Crystal structure of cisplatinated bovine Cu,Zn superoxide dismutase | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | OXIDOREDUCTASE / cisplatin / platinum / SOD / cu / zn SOD / metal based drugs / cancer / protein | ||||||
Function / homology | ![]() Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization ...Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / dendrite cytoplasm / glutathione metabolic process / embryo implantation / reactive oxygen species metabolic process / removal of superoxide radicals / 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 / response to ethanol / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Calderone, V. / Casini, A. / Mangani, S. / Messori, L. / Orioli, P.L. | ||||||
![]() | ![]() Title: Structural investigation of cisplatin-protein interactions: selective platination of His19 in a cuprozinc superoxide dismutase. Authors: Calderone, V. / Casini, A. / Mangani, S. / Messori, L. / Orioli, P.L. #1: ![]() Title: Crystallographic determination of reduced bovine superoxide dismutase at pH 5.0 and of anion binding to its active site Authors: Ferraroni, M. / Rypniewski, W.R. / Bruni, B. / Orioli, P. / Mangani, S. #2: Journal: Chem.Rev. / Year: 1999 Title: Structure, Recognition, and Processing of Cisplatin-DNA Adducts Authors: Jamieson, E.R. / Lippard, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.4 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
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Full document | ![]() | 431.2 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sxsS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The asymmetric unit contains two molecules which correspond to a physiological dimer. |
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Components
#1: Protein | Mass: 15573.337 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM Tris HCl, 18% PEG 4000, 20% 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCED ULTRA / Wavelength: 1.5418 |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jun 1, 2005 / Details: Enhance ultra, graded multilayer |
Radiation | Monochromator: Graded Multi layer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→147.44 Å / Num. all: 32303 / Num. obs: 32303 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3880 / Rsym value: 0.42 / % possible all: 81.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SXS Resolution: 1.8→44.9 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.888 / SU B: 2.972 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.127 / 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: 7.303 Å2
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Refine analyze | Luzzati sigma a obs: 0.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→44.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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