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- PDB-6l8g: High resolution structure of YoeB in complex with YefM C-terminus... -

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Basic information

Entry
Database: PDB / ID: 6l8g
TitleHigh resolution structure of YoeB in complex with YefM C-terminus(46N-83V) from Staphylococcus aureus.
Components
  • Antitoxin
  • YoeB
KeywordsANTITOXIN/TOXIN / toxin-antitoxin / microbial RNase / YoeB / TOXIN / ANTITOXIN-TOXIN complex
Function / homology
Function and homology information


RNA catabolic process / endonuclease activity / sequence-specific DNA binding / hydrolase activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / RNA binding
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 / Toxin YoeB
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsYue, J. / Xue, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaU1632124 to L.N. China
CitationJournal: To Be Published
Title: Structural insight into the mechanism of conditional cooperativity in the YoeB-YefM toxin-antitoxin system
Authors: Xue, L. / Yue, J.
History
DepositionNov 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antitoxin
B: YoeB


Theoretical massNumber of molelcules
Total (without water)14,7652
Polymers14,7652
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-17 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.206, 58.117, 65.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein/peptide Antitoxin


Mass: 4306.786 Da / Num. of mol.: 1 / Fragment: C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_02692 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2G285
#2: Protein YoeB


Mass: 10457.985 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_02691 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2G286
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 5% v/v Tacsimate pH 7.0 0.1 M HEPES pH 7.0 10% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 64910 / % possible obs: 99.3 % / Redundancy: 11.8 % / Biso Wilson estimate: 6.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.011 / Rrim(I) all: 0.04 / Net I/σ(I): 61.6
Reflection shellResolution: 1→1.02 Å / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 3023 / CC1/2: 0.996 / Rpim(I) all: 0.063 / Rrim(I) all: 0.187

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→43.5 Å / SU ML: 0.0847 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 14.5732
RfactorNum. reflection% reflection
Rfree0.1758 3248 5.01 %
Rwork0.1679 --
obs0.1683 64824 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 8.5 Å2
Refinement stepCycle: LAST / Resolution: 1→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 0 177 1199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391039
X-RAY DIFFRACTIONf_angle_d0.75431395
X-RAY DIFFRACTIONf_chiral_restr0.0783150
X-RAY DIFFRACTIONf_plane_restr0.0047181
X-RAY DIFFRACTIONf_dihedral_angle_d13.1342402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.22661250.24422423X-RAY DIFFRACTION91.39
1.01-1.030.18961520.2042617X-RAY DIFFRACTION98.79
1.03-1.050.18961490.17492644X-RAY DIFFRACTION99.86
1.05-1.070.17131340.15822681X-RAY DIFFRACTION99.82
1.07-1.080.15211210.15152656X-RAY DIFFRACTION99.25
1.08-1.110.15411370.14212647X-RAY DIFFRACTION99.25
1.11-1.130.11661350.14132638X-RAY DIFFRACTION99.6
1.13-1.150.15571470.14172690X-RAY DIFFRACTION99.89
1.15-1.180.13331400.14462647X-RAY DIFFRACTION99.5
1.18-1.210.17041290.14922686X-RAY DIFFRACTION99.61
1.21-1.240.15581410.14932642X-RAY DIFFRACTION98.72
1.24-1.280.1651440.15482635X-RAY DIFFRACTION99.82
1.28-1.320.15811300.15392709X-RAY DIFFRACTION99.75
1.32-1.370.15531480.15792675X-RAY DIFFRACTION99.65
1.37-1.420.16421310.15872704X-RAY DIFFRACTION99.86
1.42-1.490.15571320.15742686X-RAY DIFFRACTION99.23
1.49-1.560.1541260.15162704X-RAY DIFFRACTION99.58
1.56-1.660.17791490.15522691X-RAY DIFFRACTION99.89
1.66-1.790.1691640.16752689X-RAY DIFFRACTION99.83
1.79-1.970.17721540.17932707X-RAY DIFFRACTION99.51
1.97-2.260.18691420.17682744X-RAY DIFFRACTION99.62
2.26-2.840.20541570.19792766X-RAY DIFFRACTION99.93
2.84-43.50.1961610.17532895X-RAY DIFFRACTION99.67

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