+Open data
-Basic information
Entry | Database: PDB / ID: 3t5w | ||||||
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Title | 2ME modified human SOD1 | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / 2ME modification at Cys111 | ||||||
Function / homology | Function and homology information action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ihara, K. / Yamaguchi, Y. / Torigoe, H. / Wakatsuki, S. / Taniguchi, N. / Suzuki, K. / Fujiwara, N. | ||||||
Citation | Journal: Biosci.Rep. / Year: 2012 Title: Structural switching of Cu,Zn-superoxide dismutases at loop VI: insights from the crystal structure of 2-mercaptoethanol-modified enzyme Authors: Ihara, K. / Fujiwara, N. / Yamaguchi, Y. / Torigoe, H. / Wakatsuki, S. / Taniguchi, N. / Suzuki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t5w.cif.gz | 379.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t5w.ent.gz | 309.6 KB | Display | PDB format |
PDBx/mmJSON format | 3t5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t5w ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t5w | HTTPS FTP |
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-Related structure data
Related structure data | 1p1vS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15903.680 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase #2: Chemical | ChemComp-CU1 / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: 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: 2.75 Å3/Da / Density % sol: 55.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15% PEG 3350, 300mM (NH4)2SO4, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2008 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→118.7 Å / Num. all: 195308 / Num. obs: 185279 / % possible obs: 94.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.115 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 17868 / Rsym value: 0.882 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1p1v Resolution: 1.8→34.04 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.564 / SU ML: 0.092 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.132 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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 |
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