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Open data
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Basic information
Entry | Database: PDB / ID: 3gtv | ||||||
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Title | Human-mouse SOD1 chimera | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | OXIDOREDUCTASE / human / MOUSE CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / Disease mutation / Disulfide bond / 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 / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of protein kinase activity / 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 / response to copper ion / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / superoxide dismutase / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / transmission of nerve impulse / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / glutathione metabolic process / embryo implantation / : / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / response to nutrient levels / 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 / response to hydrogen peroxide / placenta development / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / Platelet degranulation / peroxisome / myelin sheath / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / response to oxidative stress / positive regulation of MAPK cascade / lysosome / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / negative regulation of apoptotic process / apoptotic process / enzyme binding / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm 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 | ![]() | 375.9 KB | Display | ![]() |
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PDB format | ![]() | 305 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3gttC ![]() 3ltvC ![]() 2vr7S ![]() 3gtw C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15911.709 Da / Num. of mol.: 12 Fragment: residues 2-81 from human protein, residues 82-154 from mouse protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: SOD1 / Plasmid: pKA8H / Production host: ![]() ![]() References: UniProt: P00441, UniProt: P08228, 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: 4.15 Å3/Da / Density % sol: 70.36 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 0.1 m HEPES, 25% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 12, 2008 / Details: MIRRORS |
Radiation | Monochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection twin | Operator: l,-k,h / Fraction: 0.124 |
Reflection | Resolution: 2.198→50 Å / Num. obs: 148445 / % possible obs: 94 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.7 Å2 / Rsym value: 0.111 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.476 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VR7 Resolution: 2.2→40.35 Å / Isotropic thermal model: isotropic / σ(F): 1.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.2 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40.35 Å
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Refine LS restraints |
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LS refinement shell |
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