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- PDB-1rk7: Solution structure of apo Cu,Zn Superoxide Dismutase: role of met... -

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Basic information

Entry
Database: PDB / ID: 1rk7
TitleSolution structure of apo Cu,Zn Superoxide Dismutase: role of metal ions in protein folding
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / 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 / 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 / superoxide anion generation / retina homeostasis / 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 / 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 / regulation of multicellular organism growth / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / sensory perception of sound / 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 / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, restrained energy minimization in vacuum
AuthorsBanci, L. / Bertini, I. / Cramaro, F. / Del Conte, R. / Viezzoli, M.S.
CitationJournal: 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
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)15,8321
Polymers15,8321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 400structures with the lowest energy,target function
Representative

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
113CBCA(CO)NH, HN(CA)CB,HNCO,HN(CA)CO,13C H(C)CH-TOCSY,13CC(CO)NH-TOCSY,13C NOESY-HSQC
122HNHA,HNHB,15N HSQC NOESY,15N HSQC
1312D NOESY
NMR detailsText: The solution structure of Apo SOD was determined using triple resonance three and bi dimensional and homonuclear bidimensional techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
1Apo SOD 2mM20mM phosphate buffer pH5.0, 10% D2O
2Apo SOD 2mM enriched in 15N20mM phosphate buffer pH5.0, 10% D2O
3Apo SOD 2mM enriched in 15N and 13C20mM phosphate buffer pH5.0, 10% D2O
Sample conditionspH: 5.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
CALIBAGuenter et al.structure solution
GLOMSAGuenter et al.structure solution
DYANAGuenter et al.structure solution
AmberPearlman et al.refinement
XwinNMRcollection
PROCHECK-NMR AQUALaskowski et al.data analysis
RefinementMethod: 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 ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 400 / Conformers submitted total number: 30

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