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- PDB-8yzg: Antitoxin protein from S. pneumoniae -

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Basic information

Entry
Database: PDB / ID: 8yzg
TitleAntitoxin protein from S. pneumoniae
ComponentsAntitoxin
KeywordsANTITOXIN / Antitoxin protein
Function / homology: / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / Antitoxin
Function and homology information
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKim, D.H. / Kang, S.M. / 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 6, 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

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Assembly

Deposited unit
A: Antitoxin


Theoretical massNumber of molelcules
Total (without water)6,9801
Polymers6,9801
Non-polymers00
Water91951
1
A: Antitoxin

A: Antitoxin


Theoretical massNumber of molelcules
Total (without water)13,9602
Polymers13,9602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2280 Å2
ΔGint-24 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.273, 37.273, 89.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Antitoxin


Mass: 6979.872 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.899995 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899995 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 23751 / % possible obs: 99.1 % / Redundancy: 13.036 % / Biso Wilson estimate: 11.84 Å2 / CC1/2: 0.999 / Net I/σ(I): 49.81
Reflection shellResolution: 1.4→1.48 Å / Num. unique obs: 3673 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→34.43 Å / SU ML: 0.0767 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.3761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 656 5 %
Rwork0.2151 12460 -
obs0.2162 13116 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.43 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms489 0 0 51 540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006497
X-RAY DIFFRACTIONf_angle_d0.8424671
X-RAY DIFFRACTIONf_chiral_restr0.073676
X-RAY DIFFRACTIONf_plane_restr0.004686
X-RAY DIFFRACTIONf_dihedral_angle_d3.469191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.510.19481220.19322335X-RAY DIFFRACTION95.23
1.51-1.660.2151290.19562448X-RAY DIFFRACTION100
1.66-1.90.20461320.20262488X-RAY DIFFRACTION99.96
1.9-2.390.23481320.2062514X-RAY DIFFRACTION100
2.39-34.430.25671410.23112675X-RAY DIFFRACTION99.96

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