+Open data
-Basic information
Entry | Database: PDB / ID: 2gbv | ||||||
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Title | C6A/C111A/C57A/C146A holo CuZn Superoxide dismutase | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / HUMAN CU/ZN SUPEROXIDE DISMUTASE / CYSTEIN-FREE | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Hornberg, A. / Logan, D.T. / Marklund, S.L. / Oliveberg, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Coupling between Disulphide Status, Metallation and Dimer Interface Strength in Cu/Zn Superoxide Dismutase Authors: Hornberg, A. / Logan, D.T. / Marklund, S.L. / Oliveberg, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gbv.cif.gz | 309.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gbv.ent.gz | 250.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gbv_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 2gbv_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | 2gbv_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 2gbv_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/2gbv ftp://data.pdbj.org/pub/pdb/validation_reports/gb/2gbv | HTTPS FTP |
-Related structure data
Related structure data | 2gbtC 2gbuC 1n18S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 15699.299 Da / Num. of mol.: 10 / Mutation: C6A/C111A/C57A/C146A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pACA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P00441, superoxide dismutase #2: Chemical | ChemComp-CU1 / #3: Chemical | ChemComp-ZN / #4: 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: 3.86 Å3/Da / Density % sol: 68.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.8M Ammonium Sulphate, 50mM NaAc, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 26, 2004 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 162729 / Num. obs: 162729 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 8.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1N18 Resolution: 2→19.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.274 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.12 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.336 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153
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