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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 / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / relaxation of vascular associated smooth muscle / dense core granule / regulation of organ growth / response to superoxide / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / relaxation of vascular associated smooth muscle / dense core granule / regulation of organ growth / response to superoxide / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / anterograde axonal transport / protein phosphatase 2B binding / regulation of T cell differentiation in thymus / Oxidoreductases; Acting on a sulfur group of donors / regulation of GTPase activity / retina homeostasis / auditory receptor cell stereocilium organization / cellular response to potassium ion / hydrogen peroxide biosynthetic process / retrograde axonal transport / myeloid cell homeostasis / superoxide anion generation / superoxide metabolic process / response to copper ion / superoxide dismutase / muscle cell cellular homeostasis / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / heart contraction / cellular response to ATP / cellular response to cadmium ion / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / ovarian follicle development / neuronal action potential / positive regulation of superoxide anion generation / axon cytoplasm / removal of superoxide radicals / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of phagocytosis / dendrite cytoplasm / placenta development / thymus development / positive regulation of cytokine production / regulation of mitochondrial membrane potential / determination of adult lifespan / response to amphetamine / glutathione metabolic process / response to hydrogen peroxide / locomotory behavior / sensory perception of sound / response to nutrient levels / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / response to ethanol / positive regulation of MAPK cascade / lysosome / positive regulation of apoptotic process / response to xenobiotic stimulus / mitochondrial matrix / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / : / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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:
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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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