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- PDB-4b3e: Structure of copper-zinc superoxide dismutase complexed with bica... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b3e | ||||||
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Title | Structure of copper-zinc superoxide dismutase complexed with bicarbonate. | ||||||
![]() | SUPEROXIDE DISMUTASE [CU-ZN] | ||||||
![]() | OXIDOREDUCTASE | ||||||
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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...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 / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / transmission of nerve impulse / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / glutathione 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 / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / 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 / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Strange, R.W. / Hough, M.A. / Antonyuk, S.V. / Hasnain, S.S. | ||||||
![]() | ![]() Title: Structural Evidence for a Copper-Bound Carbonate Intermediate in the Peroxidase and Dismutase Activities of Superoxide Dismutase. Authors: Strange, R.W. / Hough, M.A. / Antonyuk, S.V. / Hasnain, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 584.6 KB | Display | ![]() |
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PDB format | ![]() | 486.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 509.7 KB | Display | ![]() |
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Full document | ![]() | 517.1 KB | Display | |
Data in XML | ![]() | 72.8 KB | Display | |
Data in CIF | ![]() | 105.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sosS ![]() 4a7r 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 15958.757 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1622 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CO3 / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 1 M AMMONIUM SULPHATE, 50 MM TRIS PH 8.0 AND 50 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2007 / Details: MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 124983 / % possible obs: 94.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SOS Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.871 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.335 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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