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Yorodumi- PDB-1dsw: THE SOLUTION STRUCTURE OF A MONOMERIC, REDUCED FORM OF HUMAN COPP... -
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-Basic information
Entry | Database: PDB / ID: 1dsw | ||||||
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Title | THE SOLUTION STRUCTURE OF A MONOMERIC, REDUCED FORM OF HUMAN COPPER, ZINC SUPEROXIDE DISMUTASE BEARING THE SAME CHARGE AS THE NATIVE PROTEIN | ||||||
Components | SUPEROXIDE DISMUTASE (CU-ZN) | ||||||
Keywords | OXIDOREDUCTASE / REDUCED COPPER-ZINC-PROTEIN / BETA BARREL / SINGLE ALPHA HELIX | ||||||
Function / homology | Function and homology information action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / regulation of organ growth / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / regulation of organ growth / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / superoxide anion generation / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / regulation of GTPase activity / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / removal of superoxide radicals / 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 / axon cytoplasm / ovarian follicle development / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / response to organic substance / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / small GTPase binding / peroxisome / Platelet degranulation / gene expression / response to heat / cytoplasmic vesicle / protein-folding chaperone binding / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / 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 / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / THE NMR STRUCTURE CALCULATION PROGRAM USED DYANA THAT USES SIMULATED ANNEALING, MOLECULAR DYNAMICS IN TORSION ANGLE SPACE (TORSION ANGLE DYNAMICS) | ||||||
Authors | Banci, L. / Bertini, I. / Del Conte, R. / Fadin, R. / Mangani, S. / Viezzoli, M.S. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1999 Title: The solution structure of a monomeric, reduced form of human copper,zinc superoxide dismutase bearing the same charge as the native protein. Authors: Banci, L. / Bertini, I. / Del Conte, R. / Fadin, R. / Mangani, S. / 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 | 1dsw.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dsw.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/1dsw ftp://data.pdbj.org/pub/pdb/validation_reports/ds/1dsw | HTTPS FTP |
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-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: 15879.502 Da / Num. of mol.: 1 Fragment: M4SOD IS A MONOMERIC VARIANT OF HUMAN SOD. THE MUTANT IS STUDIED IN THE REDUCED FORM, EACH MOLECULE CONTAINS A CU(I) AND A ZN(II) IONS. Mutation: YES Source method: isolated from a genetically manipulated source Details: COPPER, ZINC SUPEROXIDE DISMUTASE (SOD) IS AN ENZYME WHICH CATALYZES THE DISMUTATION OF SUPEROXIDE Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase |
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#2: Chemical | ChemComp-CU / |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 2MM M4SOD FULLY ENRICHED IN 15N; 20MM PHOSPHATE BUFFER PH 5.0; 90% H2O, 10% D2O. THE PROTEIN WAS REDUCED WITH SODIUM ISOASCORBATE UNDER UNAEROBIC CONDITIONS. |
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Sample conditions | pH: 5.00 / Pressure: ATMOSPHERIC atm / Temperature: 298.00 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: THE NMR STRUCTURE CALCULATION PROGRAM USED DYANA THAT USES SIMULATED ANNEALING, MOLECULAR DYNAMICS IN TORSION ANGLE SPACE (TORSION ANGLE DYNAMICS) Software ordinal: 1 Details: INTENSITIES OF DIPOLAR CONNECTIVITIES IN 3D NOESY-HSQC, 3D HNHA AND 2D NOESY WERE MEASURED WITH THE INTEGRATION ROUTINES OF THE PROGRAM XEASY. PEAK VOLUMES WERE CONVERTED INTO UPPER DISTANCE ...Details: INTENSITIES OF DIPOLAR CONNECTIVITIES IN 3D NOESY-HSQC, 3D HNHA AND 2D NOESY WERE MEASURED WITH THE INTEGRATION ROUTINES OF THE PROGRAM XEASY. PEAK VOLUMES WERE CONVERTED INTO UPPER DISTANCE LIMITS BY FOLLOWING THE METHODOLOGY OF THE PROGRAM CALIBA. 3JHNHA COUPLING CONSTANTS WERE OBTAINED FROM THE RATIO BETWEEN THE INTENSITY OF THE DIAGONAL PEAK AND THAT OF THE CROSS PEAK OF THE 3D HNHA EXPERIMENT. THE 3D STRUCTURE WAS CALCULATED WITH THE PROGRAM DYANA; THE FINAL DYANA FAMILY WAS FORMED BY THE 36 CONFORMERS WITH THE LOWEST TARGET FUNCTION. REFINEMENT WAS PERFORMED THROUGH RESTRAINED ENERGY MINIMIZATION WITH THE SANDER MODULE OF THE PROGRAM AMBER. NOESY CROSS PEAKS WERE BACK -CALCULATED ON THE FINAL STRUCTURE WITH THE PROGRAM CORMA. | ||||||||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |