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- PDB-7fb6: C57D/C146D mutant of Human Cu, Zn Superoxide Dismutase (SOD1) -

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Basic information

Entry
Database: PDB / ID: 7fb6
TitleC57D/C146D mutant of Human Cu, Zn Superoxide Dismutase (SOD1)
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / Superoxide / oxidation / metalloprotein / hydrogen peroxide / filament / ALS
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / regulation of organ growth / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / regulation of organ growth / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / regulation of GTPase activity / 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 / ectopic germ cell programmed cell death / regulation of multicellular organism growth / neuronal action potential / response to axon injury / 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 / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / determination of adult lifespan / positive regulation of cytokine production / locomotory behavior / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / peroxisome / Platelet degranulation / 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 / positive regulation of apoptotic process / response to xenobiotic stimulus / 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
Copper/Zinc superoxide dismutase signature 1. / 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 (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBaek, Y. / Ha, N.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2022
Title: Structural analysis of the overoxidized Cu/Zn-superoxide dismutase in ROS-induced ALS filament formation.
Authors: Baek, Y. / Woo, T.G. / Ahn, J. / Lee, D. / Kwon, Y. / Park, B.J. / Ha, N.C.
History
DepositionJul 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,7867
Polymers33,4932
Non-polymers2935
Water2,792155
1
A: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9114
Polymers16,7461
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area7750 Å2
MethodPISA
2
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8753
Polymers16,7461
Non-polymers1292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-13 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.319, 48.554, 55.015
Angle α, β, γ (deg.)90.000, 93.168, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 16746.461 Da / Num. of mol.: 2 / Mutation: C57D/C146D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.36 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M MgCl2, 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 23316 / % possible obs: 96.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 16.95 Å2 / CC1/2: 0.976 / Rpim(I) all: 0.045 / Rrim(I) all: 0.113 / Χ2: 0.972 / Net I/σ(I): 11.9671
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.79 / Num. unique obs: 996 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.139 / Rrim(I) all: 0.297 / Χ2: 1.133 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PU0

1pu0


Resolution: 1.8→36.38 Å / SU ML: 0.169 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 20.5725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213 1024 4.81 %
Rwork0.1843 20276 -
obs0.1856 21300 88.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.86 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 5 155 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842241
X-RAY DIFFRACTIONf_angle_d1.10413023
X-RAY DIFFRACTIONf_chiral_restr0.0744330
X-RAY DIFFRACTIONf_plane_restr0.0072410
X-RAY DIFFRACTIONf_dihedral_angle_d14.8810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.90.2498900.2091910X-RAY DIFFRACTION58.46
1.9-2.020.20831420.19382359X-RAY DIFFRACTION73.32
2.02-2.170.26111590.19872942X-RAY DIFFRACTION90.17
2.17-2.390.22591430.20163192X-RAY DIFFRACTION97.06
2.39-2.740.25941490.20433271X-RAY DIFFRACTION98.9
2.74-3.450.21741950.19463257X-RAY DIFFRACTION99.48
3.45-36.380.15961460.15473345X-RAY DIFFRACTION99.12

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