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Open data
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Basic information
Entry | Database: PDB / ID: 3ltv | ||||||
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Title | Mouse-human sod1 chimera | ||||||
![]() | Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn] | ||||||
![]() | OXIDOREDUCTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / DISEASE MUTATION / PHOSPHOPROTEIN | ||||||
Function / homology | ![]() Detoxification of Reactive Oxygen Species / dense core granule / Platelet degranulation / action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide ...Detoxification of Reactive Oxygen Species / dense core granule / Platelet degranulation / action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / response to copper ion / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / positive regulation of catalytic activity / superoxide dismutase / negative regulation of reproductive process / negative regulation of developmental process / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / removal of superoxide radicals / response to nutrient levels / glutathione metabolic process / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / secretory granule / positive regulation of cytokine production / locomotory behavior / response to reactive oxygen species / determination of adult lifespan / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / Platelet degranulation / peroxisome / myelin sheath / gene expression / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / response to oxidative stress / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / lysosome / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / negative regulation of apoptotic process / enzyme binding / protein-containing complex / mitochondrion / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seetharaman, S.V. / Taylor, A.B. / Hart, P.J. | ||||||
![]() | ![]() Title: Structures of mouse SOD1 and human/mouse SOD1 chimeras. Authors: Seetharaman, S.V. / Taylor, A.B. / Holloway, S. / Hart, P.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 | ![]() | 174.7 KB | Display | ![]() |
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PDB format | ![]() | 140.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.5 KB | Display | ![]() |
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Full document | ![]() | 477.6 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 48 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gttC ![]() 3gtvC ![]() 2vr7S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 15750.348 Da / Num. of mol.: 6 Fragment: RESIDUES 2-81 FROM MOUSE PROTEIN, RESIDUES 82-154 FROM HUMAN PROTEIN,RESIDUES 2-81 FROM MOUSE PROTEIN, RESIDUES 82-154 FROM HUMAN PROTEIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: Sod1, SOD1 / Plasmid: PKA8H / Production host: ![]() ![]() References: UniProt: P08228, UniProt: P00441, superoxide dismutase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M SODIUM ACETATE, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2009 / Details: MIRRORS |
Radiation | Monochromator: SINGLE CRYSTAL SIDE-BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 34238 / % possible obs: 98.7 % / Redundancy: 5 % / Biso Wilson estimate: 38.4 Å2 / Rsym value: 0.103 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.55 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VR7 Resolution: 2.453→37.557 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.425 Å2 / ksol: 0.355 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.453→37.557 Å
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Refine LS restraints |
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LS refinement shell |
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