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- PDB-8kb3: Superoxide dismutase -

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Basic information

Entry
Database: PDB / ID: 8kb3
TitleSuperoxide dismutase
ComponentsSuperoxide dismutase [Mn]
KeywordsOXIDOREDUCTASE / Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems / Dimer.
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / metal ion binding / cytoplasm
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
: / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsZhai, L. / Li, B.Q. / Jia, H.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No.31900124 China
CitationJournal: To be published
Title: YdiU regulates Salmonella Oxidative Stress by UMPylation of SodA
Authors: Zhai, L. / Li, B.Q. / Jia, H.H.
History
DepositionAug 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,42518
Polymers46,2202
Non-polymers1,20516
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-42 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.026, 45.128, 92.508
Angle α, β, γ (deg.)90.000, 90.160, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Superoxide dismutase [Mn]


Mass: 23110.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: sodA, STM4055 / Production host: Escherichia coli (E. coli) / References: UniProt: P43019, superoxide dismutase

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Non-polymers , 5 types, 454 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1.8 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 50682 / % possible obs: 95.18 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.68
Reflection shellResolution: 1.61→1.67 Å / Rmerge(I) obs: 0.166 / Num. unique obs: 4201

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→26.28 Å / SU ML: 0.1428 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2055 2557 5.05 %
Rwork0.1737 48088 -
obs0.1752 50645 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.46 Å2
Refinement stepCycle: LAST / Resolution: 1.62→26.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 68 438 3744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923382
X-RAY DIFFRACTIONf_angle_d1.03684582
X-RAY DIFFRACTIONf_chiral_restr0.0565480
X-RAY DIFFRACTIONf_plane_restr0.0065589
X-RAY DIFFRACTIONf_dihedral_angle_d6.9825450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.22241080.19592382X-RAY DIFFRACTION87.09
1.65-1.680.20221170.18462541X-RAY DIFFRACTION89.49
1.68-1.720.23921800.18132524X-RAY DIFFRACTION92.54
1.72-1.760.23731500.18222591X-RAY DIFFRACTION94.22
1.76-1.80.2431500.17692700X-RAY DIFFRACTION95.99
1.8-1.850.22031450.18162720X-RAY DIFFRACTION97.02
1.85-1.90.22261320.19592693X-RAY DIFFRACTION97.01
1.9-1.960.20761510.16922657X-RAY DIFFRACTION95.15
1.96-2.040.1991420.17192524X-RAY DIFFRACTION90.74
2.04-2.120.1941400.16872755X-RAY DIFFRACTION98
2.12-2.210.22161570.18612711X-RAY DIFFRACTION97.98
2.21-2.330.24061310.17782782X-RAY DIFFRACTION97.75
2.33-2.480.20241560.18212728X-RAY DIFFRACTION97.7
2.48-2.670.21171510.17632733X-RAY DIFFRACTION96.91
2.67-2.930.21511250.18592648X-RAY DIFFRACTION92.99
2.93-3.360.18971380.17982797X-RAY DIFFRACTION98.69
3.36-4.230.17491400.1522822X-RAY DIFFRACTION98.8
4.23-26.280.18731440.15532780X-RAY DIFFRACTION95.09

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