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Open data
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Basic information
Entry | Database: PDB / ID: 6dtk | ||||||
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Title | Heterodimers of FALS mutant SOD enzyme | ||||||
![]() | Superoxide dismutase C111S/D83S-C111S HETERODIMER | ||||||
![]() | OXIDOREDUCTASE / Copper/Zinc superoxide dismutase Cu / Zn-SOD1 / metal binding protein / FALS Zn-deficient SOD1 | ||||||
Function / homology | ![]() 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 ...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 / 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 / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / 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 / 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 / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Streltsov, V.A. / Nuttall, S.D. / Ganio, K.E. / Roberts, B. | ||||||
![]() | ![]() Title: Structural characterization of heterodimers of FALS mutant SOD enzyme Authors: Streltsov, V.A. / Nuttall, S.D. / Ganio, K.E. / Roberts, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 326.1 KB | Display | ![]() |
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PDB format | ![]() | 263.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1funS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32725.129 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-MLI / | #5: Water | ChemComp-HOH / | Compound details | Chimeric construct: mutated and WT protein chains are linked via linker and form a heterodimer. Due ...Chimeric construct: mutated and WT protein chains are linked via linker and form a heterodimer. Due to almost two fold symmetry of the heterodimer and structural similarity to the WT protein (or possible admixture of homodimers formed due to broken linker), the crystal electron density shows an average picture with fractional mixed DS populations on positions 83 and 252. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2-3 M Ammonium sulfate or Sodium malonate / PH range: 4.5-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2013 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.57 Å / Num. obs: 158995 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 14.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.25 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.47 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FUN Resolution: 2→47.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.021 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.112 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.57 Å
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