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- PDB-9m59: Cu/Zn-superoxide dismutase from Deinococcus radiodurans (Calcium-... -

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Basic information

Entry
Database: PDB / ID: 9m59
TitleCu/Zn-superoxide dismutase from Deinococcus radiodurans (Calcium-bound)
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: 1.9 Å
AuthorsMuraki, 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)93,58017
Polymers92,4992
Non-polymers1,08115
Water5,657314
1
A: Superoxide dismutase (SodC), Cu-Zn family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8389
Polymers46,2491
Non-polymers5898
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Superoxide dismutase (SodC), Cu-Zn family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7428
Polymers46,2491
Non-polymers4937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.278, 133.278, 76.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

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


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

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Non-polymers , 6 types, 329 molecules

#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6M Lithium Sulfate, 0.1M Tris, pH 8.0

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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: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→36.917 Å / Num. obs: 105657 / % possible obs: 99.96 % / Redundancy: 7.7 % / Biso Wilson estimate: 40.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04272 / Rpim(I) all: 0.01639 / Rrim(I) all: 0.0458 / Net I/σ(I): 24.82
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 8 % / Rmerge(I) obs: 0.939 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 10494 / CC1/2: 0.776 / Rpim(I) all: 0.3531 / Rrim(I) all: 1.004 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8refinement
PHENIX1.20.1refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.917 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 10356 5 %
Rwork0.1958 --
obs0.197 105641 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→36.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6426 0 43 314 6783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076690
X-RAY DIFFRACTIONf_angle_d0.8669130
X-RAY DIFFRACTIONf_dihedral_angle_d12.1693996
X-RAY DIFFRACTIONf_chiral_restr0.0581032
X-RAY DIFFRACTIONf_plane_restr0.0061211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.35573610.34086559X-RAY DIFFRACTION100
1.9216-1.94420.33993490.3196522X-RAY DIFFRACTION100
1.9442-1.96790.32643820.30296545X-RAY DIFFRACTION100
1.9679-1.99290.33073450.28736583X-RAY DIFFRACTION100
1.9929-2.01910.29943240.27936612X-RAY DIFFRACTION100
2.0191-2.04670.30262600.27936619X-RAY DIFFRACTION100
2.0467-2.0760.29343980.26796563X-RAY DIFFRACTION100
2.076-2.1070.27513520.26316520X-RAY DIFFRACTION100
2.107-2.13990.27743820.25836542X-RAY DIFFRACTION100
2.1399-2.1750.28024530.25646452X-RAY DIFFRACTION100
2.175-2.21250.30083400.24776540X-RAY DIFFRACTION100
2.2125-2.25270.24643150.23136646X-RAY DIFFRACTION100
2.2527-2.2960.26832880.22626606X-RAY DIFFRACTION100
2.296-2.34290.27192760.23696606X-RAY DIFFRACTION100
2.3429-2.39380.31563260.23636646X-RAY DIFFRACTION100
2.3938-2.44950.26223880.22646464X-RAY DIFFRACTION100
2.4495-2.51070.2623480.22296557X-RAY DIFFRACTION100
2.5107-2.57860.24573820.22276556X-RAY DIFFRACTION100
2.5786-2.65440.23693460.22536573X-RAY DIFFRACTION100
2.6544-2.74010.30823130.23126598X-RAY DIFFRACTION100
2.7401-2.8380.29133500.24326556X-RAY DIFFRACTION100
2.838-2.95160.25213260.2346596X-RAY DIFFRACTION100
2.9516-3.08580.27433670.22666515X-RAY DIFFRACTION100
3.0858-3.24840.25272950.23046581X-RAY DIFFRACTION100
3.2484-3.45180.22183320.20186590X-RAY DIFFRACTION99
3.4518-3.71810.20133240.18266536X-RAY DIFFRACTION100
3.7181-4.09180.17863600.16386553X-RAY DIFFRACTION100
4.0918-4.68290.15613960.13346502X-RAY DIFFRACTION100
4.6829-5.89610.15493330.13686590X-RAY DIFFRACTION100
5.8961-36.90.15973450.14766525X-RAY DIFFRACTION100

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