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Yorodumi- PDB-1rk7: Solution structure of apo Cu,Zn Superoxide Dismutase: role of met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rk7 | ||||||
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Title | Solution structure of apo Cu,Zn Superoxide Dismutase: role of metal ions in protein folding | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / apo form of monomeric mutant of Cu / Zn SOD / solution structure / Q133M2SOD | ||||||
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 energy minimization in vacuum | ||||||
Authors | Banci, L. / Bertini, I. / Cramaro, F. / Del Conte, R. / Viezzoli, M.S. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Solution structure of Apo Cu,Zn Superoxide Dismutase: Role of Metal Ions in Protein Folding Authors: Banci, L. / Bertini, I. / Cramaro, F. / Del Conte, R. / 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 | 1rk7.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1rk7.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1rk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rk7_validation.pdf.gz | 349.5 KB | Display | wwPDB validaton report |
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Full document | 1rk7_full_validation.pdf.gz | 675.3 KB | Display | |
Data in XML | 1rk7_validation.xml.gz | 118.8 KB | Display | |
Data in CIF | 1rk7_validation.cif.gz | 147.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/1rk7 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/1rk7 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15832.447 Da / Num. of mol.: 1 / Mutation: C6A, F50E, G51E, C111S, E133Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pbr322 with human sod gene / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP1 / References: UniProt: P00441, superoxide dismutase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: The solution structure of Apo SOD was determined using triple resonance three and bi dimensional and homonuclear bidimensional techniques |
-Sample preparation
Details |
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Sample conditions | pH: 5 / Pressure: 1 atm / Temperature: 298 K | ||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-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 energy minimization in vacuum Software ordinal: 1 Details: The structures were calculated using the constraints: 2382 meaningful upper distance limits, 42 dihedral phi angles, 41 dihedral psi angles and 42 proton pairs stereospecifically assigned. ...Details: The structures were calculated using the constraints: 2382 meaningful upper distance limits, 42 dihedral phi angles, 41 dihedral psi angles and 42 proton pairs stereospecifically assigned. The disulphide bridge between C57 and C146 was introduced with the upper and lower distances limits between the CB and SG atoms of the two side chains. | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy,target function Conformers calculated total number: 400 / Conformers submitted total number: 30 |