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- PDB-8zd5: Crystal structure of E40K variant of Cu/Zn-superoxide dismutase f... -

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Basic information

Entry
Database: PDB / ID: 8zd5
TitleCrystal structure of E40K variant of Cu/Zn-superoxide dismutase from dog (Canis familiaris) in the holo 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
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesMus musculus (house mouse)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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
H: 22E1VH-SARAH
F: 22E1VL-SARAH
E: 22E1VH-SARAH
A: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
B: 22E1VH-SARAH
C: 22E1VL-SARAH
L: 22E1VL-SARAH
K: 22E1VH-SARAH
I: 22E1VL-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,57220
Polymers213,05612
Non-polymers5168
Water00
1
H: 22E1VH-SARAH
G: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
L: 22E1VL-SARAH
K: 22E1VH-SARAH
I: 22E1VL-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,78610
Polymers106,5286
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 22E1VL-SARAH
E: 22E1VH-SARAH
A: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
B: 22E1VH-SARAH
C: 22E1VL-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,78610
Polymers106,5286
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.915, 82.213, 187.612
Angle α, β, γ (deg.)90.00, 108.46, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: 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)
#2: 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)
#3: 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
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
Has ligand of interestN
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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% (w/v) polyethylene glycol 4000, 0.1M Tris pH 8.5, 0.2M lithium 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: Nov 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.89→48.11 Å / Num. obs: 53258 / % possible obs: 97.8 % / Redundancy: 3.4 % / CC1/2: 1 / Rpim(I) all: 0.061 / Net I/σ(I): 7.9
Reflection shellResolution: 2.89→2.98 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4024 / CC1/2: 0.58 / Rpim(I) all: 0.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→48.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.199 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24921 2671 5 %RANDOM
Rwork0.20106 ---
obs0.20347 50587 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.162 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å20.58 Å2
2--4.11 Å20 Å2
3----6.64 Å2
Refinement stepCycle: 1 / Resolution: 2.89→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14151 0 8 0 14159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01214458
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613341
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.65119535
X-RAY DIFFRACTIONr_angle_other_deg0.3771.57630874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88351832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.016566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.848102474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0510.22134
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023122
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_it7.5139.6267391
X-RAY DIFFRACTIONr_mcbond_other7.5069.6267391
X-RAY DIFFRACTIONr_mcangle_it11.3917.2889202
X-RAY DIFFRACTIONr_mcangle_other11.3917.2889203
X-RAY DIFFRACTIONr_scbond_it8.87110.4317067
X-RAY DIFFRACTIONr_scbond_other8.87110.4317068
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.90318.83710334
X-RAY DIFFRACTIONr_long_range_B_refined16.97994.7815099
X-RAY DIFFRACTIONr_long_range_B_other16.9894.7815100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.894→2.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 175 -
Rwork0.365 3404 -
obs--89.9 %

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