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- PDB-9m58: Cu/Zn-superoxide dismutase from Deinococcus radiodurans (Calcium-free) -

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Basic information

Entry
Database: PDB / ID: 9m58
TitleCu/Zn-superoxide dismutase from Deinococcus radiodurans (Calcium-free)
ComponentsSuperoxide dismutase (SodC), Cu-Zn family
KeywordsMETAL BINDING PROTEIN / superoxide dismutase / beta-propeller lactonase
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / copper ion binding
Similarity search - Function
Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAkutsu, M. / Muraki, N. / Megata, M. / Furukawa, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H05765 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)22H02768 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)22K19389 Japan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Cu/Zn-superoxide dismutase naturally fused with a beta-propeller lactonase in Deinococcus radiodurans.
Authors: Furukawa, Y. / Megata, M. / Shintani, A. / Sue, K. / Morohoshi, T. / Akutsu, M. / Muraki, N.
History
DepositionMar 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase (SodC), Cu-Zn family
B: Superoxide dismutase (SodC), Cu-Zn family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7185
Polymers92,4992
Non-polymers2193
Water9,854547
1
A: Superoxide dismutase (SodC), Cu-Zn family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4053
Polymers46,2491
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16320 Å2
MethodPISA
2
B: Superoxide dismutase (SodC), Cu-Zn family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3132
Polymers46,2491
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.067, 83.067, 119.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Superoxide dismutase (SodC), Cu-Zn family / Cu/Zn-superoxide dismutase


Mass: 46249.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gly1 and Pro2 are the expression tag after cleavage.
Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Gene: DR_A0202 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RYV4
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20%(w/v) PEG 3350, 0.2M Sodium malonate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.28157 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28157 Å / Relative weight: 1
ReflectionResolution: 1.8→45.51 Å / Num. obs: 73933 / % possible obs: 98.7 % / Redundancy: 13.7 % / Biso Wilson estimate: 26.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.452 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 10648 / CC1/2: 0.816 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.89 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 3664 4.96 %
Rwork0.1635 --
obs0.1652 73903 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 8 547 6407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.053
X-RAY DIFFRACTIONf_dihedral_angle_d16.2142175
X-RAY DIFFRACTIONf_chiral_restr0.074940
X-RAY DIFFRACTIONf_plane_restr0.0111067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.32411430.24962668X-RAY DIFFRACTION97
1.82-1.850.27591160.23112673X-RAY DIFFRACTION97
1.85-1.880.2741480.20642628X-RAY DIFFRACTION97
1.88-1.90.25441180.1952670X-RAY DIFFRACTION97
1.9-1.930.20871140.18582745X-RAY DIFFRACTION98
1.93-1.960.18541490.17762620X-RAY DIFFRACTION98
1.96-20.2331510.1782664X-RAY DIFFRACTION98
2-2.030.21051290.17532664X-RAY DIFFRACTION98
2.03-2.070.19441220.1782727X-RAY DIFFRACTION98
2.07-2.120.221290.16732679X-RAY DIFFRACTION98
2.12-2.160.20181510.1632672X-RAY DIFFRACTION98
2.16-2.210.22361370.16912699X-RAY DIFFRACTION99
2.21-2.270.20541740.16242694X-RAY DIFFRACTION99
2.27-2.330.21471290.16862695X-RAY DIFFRACTION99
2.33-2.40.2351420.16432682X-RAY DIFFRACTION99
2.4-2.470.22471270.17262720X-RAY DIFFRACTION99
2.48-2.560.22511490.17242706X-RAY DIFFRACTION99
2.56-2.670.18911410.17472735X-RAY DIFFRACTION99
2.67-2.790.2381610.18362705X-RAY DIFFRACTION99
2.79-2.930.23471570.18332703X-RAY DIFFRACTION100
2.93-3.120.22391420.17522716X-RAY DIFFRACTION100
3.12-3.360.19421560.1782738X-RAY DIFFRACTION100
3.36-3.70.1661540.15552732X-RAY DIFFRACTION100
3.7-4.230.19071590.13852731X-RAY DIFFRACTION100
4.23-5.330.14251480.12742749X-RAY DIFFRACTION100
5.33-41.890.16311180.15792824X-RAY DIFFRACTION100

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