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- PDB-7wx0: E40K variant of Cu/Zn-superoxide dismutase from dog (Canis familiaris) -

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Basic information

Entry
Database: PDB / ID: 7wx0
TitleE40K variant of Cu/Zn-superoxide dismutase from dog (Canis familiaris)
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsMETAL BINDING PROTEIN / Superoxide dismutase / SOD / SOD1 / OXIDOREDUCTASE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / reactive oxygen species metabolic process / removal of superoxide radicals / peroxisome / copper ion binding / mitochondrion / nucleus / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsNarikiyo, S. / Furukawa, Y. / Akutsu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H05765 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Intrinsic structural vulnerability in the hydrophobic core induces species-specific aggregation of canine SOD1 with degenerative myelopathy-linked E40K mutation.
Authors: Hashimoto, K. / Watanabe, S. / Akutsu, M. / Muraki, N. / Kamishina, H. / Furukawa, Y. / Yamanaka, K.
History
DepositionFeb 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)31,9876
Polymers31,7302
Non-polymers2584
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-11 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.781, 50.677, 185.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15864.773 Da / Num. of mol.: 2 / Mutation: E40K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SOD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WNN6, 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 / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Sodium Malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.275 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.275 Å / Relative weight: 1
ReflectionResolution: 1.4→48.89 Å / Num. obs: 70224 / % possible obs: 95.7 % / Redundancy: 18.4 % / CC1/2: 1 / Net I/σ(I): 26.6
Reflection shellResolution: 1.4→1.48 Å / Num. unique obs: 8778 / CC1/2: 0.915

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→48.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.023 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19061 3489 5 %RANDOM
Rwork0.17078 ---
obs0.17174 66649 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.059 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å2-0 Å20 Å2
2---0.17 Å2-0 Å2
3----1.8 Å2
Refinement stepCycle: 1 / Resolution: 1.4→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 4 326 2548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132279
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172140
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.6323071
X-RAY DIFFRACTIONr_angle_other_deg1.5541.5914957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32924.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.994158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02470
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7771.9361235
X-RAY DIFFRACTIONr_mcbond_other1.7731.9361233
X-RAY DIFFRACTIONr_mcangle_it2.5992.8991542
X-RAY DIFFRACTIONr_mcangle_other2.5992.8991543
X-RAY DIFFRACTIONr_scbond_it3.6832.3111044
X-RAY DIFFRACTIONr_scbond_other3.6822.3121045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3373.2981530
X-RAY DIFFRACTIONr_long_range_B_refined6.45225.112497
X-RAY DIFFRACTIONr_long_range_B_other6.25824.3492406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 195 -
Rwork0.277 3942 -
obs--76.95 %

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