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Yorodumi- PDB-1l3n: The Solution Structure of Reduced Dimeric Copper Zinc SOD: the St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l3n | ||||||
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Title | The Solution Structure of Reduced Dimeric Copper Zinc SOD: the Structural Effects of Dimerization | ||||||
Components | superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / reduced human copper/zinc superoxide dismutase / solution structure / homodimeric protein. | ||||||
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 / 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 / positive regulation of superoxide anion generation / 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 / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / placenta development / locomotory behavior / determination of adult lifespan / sensory perception of sound / regulation of blood pressure / negative regulation of inflammatory response / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / 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 / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, restrained enegy minimization in vacuum | ||||||
Authors | Banci, L. / Bertini, I. / Cramaro, F. / Del Conte, R. / Viezzoli, M.S. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2002 Title: The solution structure of reduced dimeric copper zinc superoxide dismutase. The structural effects of dimerization Authors: Banci, L. / Bertini, I. / Cramaro, F. / Del Conte, R. / Viezzoli, M.S. #1: Journal: Biochemistry / Year: 2000 Title: Backbone dynamics of human Cu,Zn superoxide dismutase and of its monomeric F50E/G51E/E133Q mutant: the influence of dimerization on mobility and function Authors: Banci, L. / Bertini, I. / Cramaro, F. / Del Conte, R. / Rosato, A. / Viezzoli, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l3n.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1l3n.ent.gz | 2.2 MB | Display | PDB format |
PDBx/mmJSON format | 1l3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l3n_validation.pdf.gz | 373.4 KB | Display | wwPDB validaton report |
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Full document | 1l3n_full_validation.pdf.gz | 715.2 KB | Display | |
Data in XML | 1l3n_validation.xml.gz | 168.1 KB | Display | |
Data in CIF | 1l3n_validation.cif.gz | 226.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/1l3n ftp://data.pdbj.org/pub/pdb/validation_reports/l3/1l3n | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15779.430 Da / Num. of mol.: 2 / Mutation: C6A, C111S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pbr322 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP1 / References: UniProt: P00441, superoxide dismutase #2: Chemical | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Cu(I), Zn(II) SOD structure was determined using triple resonance three-and bi-dimensional and homonuclear bi-dimensional techniques. |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, restrained enegy minimization in vacuum Software ordinal: 1 Details: The structures were calculated using the constraints: 3566 NOE cross peaks were converted into distance constraints, 49 dihedral phi angles, 52 dihedral psi angles, 14 chi angles and 45 ...Details: The structures were calculated using the constraints: 3566 NOE cross peaks were converted into distance constraints, 49 dihedral phi angles, 52 dihedral psi angles, 14 chi angles and 45 proton pairs stereospecifically assigned. The Cu(I) and Zn(II) metal ions were included in the calculation with special linkers. The disulfide bridge between Cys57 and Cys146 was introduced with upper and lower distance limits between the CB and SG atoms of the two side chains. | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structure with the lowest energy target function Conformers calculated total number: 1400 / Conformers submitted total number: 30 |