+Open data
-Basic information
Entry | Database: PDB / ID: 3gtt | ||||||
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Title | Mouse SOD1 | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / MOUSE CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / Disulfide bond / Phosphoprotein | ||||||
Function / homology | Function and homology information 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 / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport ...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 / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / response to copper ion / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / embryo implantation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / response to nutrient levels / glutathione metabolic process / : / positive regulation of superoxide anion generation / 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 / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / negative regulation of inflammatory response / 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 / response to xenobiotic stimulus / 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 region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Seetharaman, S.V. / Taylor, A.B. / Hart, P.J. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gtt.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gtt.ent.gz | 150.9 KB | Display | PDB format |
PDBx/mmJSON format | 3gtt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gtt_validation.pdf.gz | 458.7 KB | Display | wwPDB validaton report |
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Full document | 3gtt_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 3gtt_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 3gtt_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/3gtt ftp://data.pdbj.org/pub/pdb/validation_reports/gt/3gtt | HTTPS FTP |
-Related structure data
Related structure data | 3gtvC 3ltvC 2vr7S 3gtw C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15834.496 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sod1 / Plasmid: pKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08228, superoxide dismutase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.31 Å3/Da / Density % sol: 71.47 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 0.1 M Tris, 30% PEG 1000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 18, 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: 1/2*h+1/2*k,3/2*h-1/2*k,-l / Fraction: 0.144 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 64203 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 29.6 Å2 / Rsym value: 0.105 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.463 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VR7 Resolution: 2.4→23.76 Å / Isotropic thermal model: isotropic / σ(F): 1.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.16 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→23.76 Å
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Refine LS restraints |
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LS refinement shell |
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