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- PDB-1dsw: THE SOLUTION STRUCTURE OF A MONOMERIC, REDUCED FORM OF HUMAN COPP... -

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Entry
Database: PDB / ID: 1dsw
TitleTHE SOLUTION STRUCTURE OF A MONOMERIC, REDUCED FORM OF HUMAN COPPER, ZINC SUPEROXIDE DISMUTASE BEARING THE SAME CHARGE AS THE NATIVE PROTEIN
ComponentsSUPEROXIDE DISMUTASE (CU-ZN)
KeywordsOXIDOREDUCTASE / REDUCED COPPER-ZINC-PROTEIN / BETA BARREL / SINGLE ALPHA HELIX
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / 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 / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / THE NMR STRUCTURE CALCULATION PROGRAM USED DYANA THAT USES SIMULATED ANNEALING, MOLECULAR DYNAMICS IN TORSION ANGLE SPACE (TORSION ANGLE DYNAMICS)
AuthorsBanci, L. / Bertini, I. / Del Conte, R. / Fadin, R. / Mangani, S. / Viezzoli, M.S.
CitationJournal: 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
DepositionJan 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: 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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE (CU-ZN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0083
Polymers15,8801
Non-polymers1292
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1

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Components

#1: Protein SUPEROXIDE DISMUTASE (CU-ZN)


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
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N NOESY-HSQC
1213D HNHA
1312D NOESY

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Sample preparation

DetailsContents: 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.
Sample conditionspH: 5 / Pressure: ATMOSPHERIC atm / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber4PEALRMAN, DA, ET AL. (1991)refinement
XwinNMR2.1structure solution
CALIBA1.5structure solution
DYANA1.4structure solution
CORMAstructure solution
RefinementMethod: 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 ensembleConformers submitted total number: 1

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