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- PDB-8zd6: Crystal structure of E40K variant of Cu/Zn-superoxide dismutase f... -

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Basic information

Entry
Database: PDB / ID: 8zd6
TitleCrystal structure of E40K variant of Cu/Zn-superoxide dismutase from dog (Canis familiaris) in the apo form complexed with 22E1 Fv-clasp
Components
  • 22E1VH-SARAH
  • 22E1VL-SARAH
  • Superoxide dismutase [Cu-Zn]
KeywordsMETAL BINDING PROTEIN / Complex / Antibody / SOD1
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / reactive oxygen species metabolic process / peroxisome / copper ion binding / mitochondrion / nucleus / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsShino, Y. / Furukawa, Y. / Muraki, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: Disulfide-mediated oligomerization of mutant Cu/Zn-superoxide dismutase associated with canine degenerative myelopathy.
Authors: Shino, Y. / Muraki, N. / Kobatake, Y. / Kamishina, H. / Kato, R. / Furukawa, Y.
History
DepositionMay 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: 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

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: 22E1VH-SARAH
C: 22E1VL-SARAH
D: Superoxide dismutase [Cu-Zn]
E: 22E1VH-SARAH
F: 22E1VL-SARAH
G: Superoxide dismutase [Cu-Zn]
H: 22E1VH-SARAH
I: 22E1VL-SARAH
J: Superoxide dismutase [Cu-Zn]
K: 22E1VH-SARAH
L: 22E1VL-SARAH


Theoretical massNumber of molelcules
Total (without water)213,05612
Polymers213,05612
Non-polymers00
Water00
1
A: Superoxide dismutase [Cu-Zn]
B: 22E1VH-SARAH
C: 22E1VL-SARAH
D: Superoxide dismutase [Cu-Zn]
E: 22E1VH-SARAH
F: 22E1VL-SARAH


Theoretical massNumber of molelcules
Total (without water)106,5286
Polymers106,5286
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Superoxide dismutase [Cu-Zn]
H: 22E1VH-SARAH
I: 22E1VL-SARAH
J: Superoxide dismutase [Cu-Zn]
K: 22E1VH-SARAH
L: 22E1VL-SARAH


Theoretical massNumber of molelcules
Total (without water)106,5286
Polymers106,5286
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.616, 83.601, 185.750
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15864.773 Da / Num. of mol.: 4 / Mutation: E40K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SOD1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle(DE3) / References: UniProt: Q8WNN6, superoxide dismutase
#2: Antibody
22E1VH-SARAH


Mass: 19194.514 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein
22E1VL-SARAH


Mass: 18204.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2% (v/v) polyethylene glycol 400, 0.1M HEPES sodium pH 7.5, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.29→47.83 Å / Num. obs: 38902 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 1 / Rpim(I) all: 0.055 / Net I/σ(I): 7.8
Reflection shellResolution: 3.29→3.42 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4189 / CC1/2: 0.59 / Rpim(I) all: 0.847

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→43.94 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.869 / SU B: 53.644 / SU ML: 0.788 / Cross valid method: THROUGHOUT / ESU R Free: 0.635 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32642 1918 4.9 %RANDOM
Rwork0.2769 ---
obs0.27938 36984 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 149.494 Å2
Baniso -1Baniso -2Baniso -3
1-20.31 Å2-0 Å24.14 Å2
2---2.89 Å2-0 Å2
3----17.85 Å2
Refinement stepCycle: 1 / Resolution: 3.29→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12453 0 0 0 12453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01112688
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611034
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.64717277
X-RAY DIFFRACTIONr_angle_other_deg0.351.57425315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76751748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.123541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.086101750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.21972
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022699
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_it12.53417.247073
X-RAY DIFFRACTIONr_mcbond_other12.53417.247073
X-RAY DIFFRACTIONr_mcangle_it19.66630.9138794
X-RAY DIFFRACTIONr_mcangle_other19.66530.9138795
X-RAY DIFFRACTIONr_scbond_it13.1917.4915615
X-RAY DIFFRACTIONr_scbond_other13.18917.4915616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other21.15931.9458484
X-RAY DIFFRACTIONr_long_range_B_refined28.717205.0450357
X-RAY DIFFRACTIONr_long_range_B_other28.717205.0450358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.29→3.371 Å
RfactorNum. reflection% reflection
Rfree0.46 144 -
Rwork0.446 2573 -
obs--94.74 %

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