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- PDB-1l3n: The Solution Structure of Reduced Dimeric Copper Zinc SOD: the St... -

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Basic information

Entry
Database: PDB / ID: 1l3n
TitleThe Solution Structure of Reduced Dimeric Copper Zinc SOD: the Structural Effects of Dimerization
Componentssuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / reduced human copper/zinc superoxide dismutase / solution structure / homodimeric protein.
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / 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 / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / 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 / 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 / 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 / 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 / small GTPase binding / regulation of blood pressure / 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
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
COPPER (I) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, restrained enegy minimization in vacuum
AuthorsBanci, 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
DepositionFeb 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: superoxide dismutase [Cu-Zn]
B: superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8176
Polymers31,5592
Non-polymers2584
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 1400structure with the lowest energy target function
Representative

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Components

#1: Protein superoxide dismutase [Cu-Zn] / SOD


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 ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3133D HNCA, 3D NH(CO)CA, 3D HNCO, 3D HN(CA)CO-TROSY like, 2D 15N-HSQC, 2D 13C-HSQC, 3D 13C-NOESY-HSQC
2223D H(C)CH-TOCSY, 3D (H)CCH-TOCSY
1313D 15N-NOESY-HSQC, 3D HNHA, 3D HNHB, 2D NOESY
4412D NOESY
1542D 15N-HSQC
NMR detailsText: Cu(I), Zn(II) SOD structure was determined using triple resonance three-and bi-dimensional and homonuclear bi-dimensional techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
1Cu(I),Zn(II) SOD 2mM enriched in 15N20mM phosphate buffer pH5.00 10% D2O, 8mM ascorbate reductant
2Cu(I),Zn(II) SOD 2mM enriched in 15N, 13C20mM phosphate buffer pH5.00 10% D2O, 8mM ascorbate reductant
3Cu(I),Zn(II) SOD 2mM enriched in 15N, 13C and 2H at 70%20mM phosphate buffer pH5.00 10% D2O, 8mM ascorbate reductant
4Cu(I),Zn(II) SOD 2mM enriched in 15N20mM phosphate buffer pH5.00 100% D2O, 8mM ascorbate reductant
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.0 1 atm296 K
45.0 1 atm286 K

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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 AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE6003

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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-NMRLaskowski et al.data analysis
RefinementMethod: 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 ensembleConformer selection criteria: structure with the lowest energy target function
Conformers calculated total number: 1400 / Conformers submitted total number: 30

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