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- PDB-8yxv: Toxin-antitoxin complex from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 8yxv
TitleToxin-antitoxin complex from Streptococcus pneumoniae
Components
  • Antitoxin
  • Putative mRNA interferase YoeB
KeywordsTOXIN / Antitoxin
Function / homology
Function and homology information


RNA catabolic process / endonuclease activity / negative regulation of DNA-templated transcription
Similarity search - Function
: / Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / Toxin-antitoxin system, RelE/ParE toxin domain superfamily
Similarity search - Domain/homology
Antitoxin / Putative mRNA interferase YoeB
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKim, D.H. / Lee, Y.C. / Jin, C. / Lee, B.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: J.Cell.Biochem. / Year: 2025
Title: Structural and Functional Insight Into YefM-YoeB Complex of Toxin-Antitoxin System From Streptococcus pneumoniae.
Authors: Kim, D.H. / Lee, Y.C. / Jin, C. / Kang, S.M. / Kang, S.J. / Kang, H.S. / Lee, B.J.
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Antitoxin
F: Putative mRNA interferase YoeB
D: Antitoxin
A: Antitoxin
E: Putative mRNA interferase YoeB
C: Antitoxin
G: Antitoxin
K: Putative mRNA interferase YoeB
I: Antitoxin
H: Antitoxin
L: Putative mRNA interferase YoeB
J: Antitoxin


Theoretical massNumber of molelcules
Total (without water)110,73012
Polymers110,73012
Non-polymers00
Water37821
1
B: Antitoxin
F: Putative mRNA interferase YoeB
D: Antitoxin
A: Antitoxin
E: Putative mRNA interferase YoeB
C: Antitoxin


Theoretical massNumber of molelcules
Total (without water)55,3656
Polymers55,3656
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Antitoxin
K: Putative mRNA interferase YoeB
I: Antitoxin
H: Antitoxin
L: Putative mRNA interferase YoeB
J: Antitoxin


Theoretical massNumber of molelcules
Total (without water)55,3656
Polymers55,3656
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.782, 63.402, 149.556
Angle α, β, γ (deg.)90.000, 128.800, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Antitoxin


Mass: 8775.974 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: SP_1741 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UR92
#2: Protein
Putative mRNA interferase YoeB


Mass: 10130.556 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: SP_1740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2URH3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ammonium sulfate,CHES/ sodium hydroxide, pH 9.5, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 38963 / % possible obs: 98.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 72.8 Å2 / CC1/2: 0.994 / Net I/σ(I): 29.6
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1938 / CC1/2: 0.805 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OEI

3oei


Resolution: 2.69→36.76 Å / SU ML: 0.3924 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 1949 5.02 %
Rwork0.22 36911 -
obs0.2219 38860 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.9 Å2
Refinement stepCycle: LAST / Resolution: 2.69→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 0 21 7227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00287351
X-RAY DIFFRACTIONf_angle_d0.59139907
X-RAY DIFFRACTIONf_chiral_restr0.03931065
X-RAY DIFFRACTIONf_plane_restr0.0041266
X-RAY DIFFRACTIONf_dihedral_angle_d4.7805937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.760.39471500.34392490X-RAY DIFFRACTION93.75
2.76-2.840.34361500.32492581X-RAY DIFFRACTION98.52
2.84-2.920.4081470.30772622X-RAY DIFFRACTION98.58
2.92-3.010.30281050.30862693X-RAY DIFFRACTION98.59
3.01-3.120.32321430.29082572X-RAY DIFFRACTION98.62
3.12-3.250.31711550.27842629X-RAY DIFFRACTION98.72
3.25-3.390.30671440.26522666X-RAY DIFFRACTION99.19
3.39-3.570.30751150.25352667X-RAY DIFFRACTION99
3.57-3.80.31581380.23182655X-RAY DIFFRACTION99.25
3.8-4.090.2581220.22182672X-RAY DIFFRACTION99.32
4.09-4.50.19451520.1882680X-RAY DIFFRACTION99.33
4.5-5.150.21991370.18282679X-RAY DIFFRACTION99.36
5.15-6.480.24351440.21012697X-RAY DIFFRACTION99.37
6.48-36.760.22641470.17492608X-RAY DIFFRACTION93.55

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