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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 / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of phagocytosis / regulation of mitochondrial membrane potential / 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 / placenta development / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / negative regulation of neuron apoptotic process / gene expression / intracellular iron ion homeostasis / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.9 KB | Display | ![]() |
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PDB format | ![]() | 263.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.8 KB | Display | ![]() |
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Full document | ![]() | 510.8 KB | Display | |
Data in XML | ![]() | 70.2 KB | Display | |
Data in CIF | ![]() | 104.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1funS 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 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. | Has protein modification | Y | |
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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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