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- PDB-7cua: The structure of YoeB dimer from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 7cua
TitleThe structure of YoeB dimer from Staphylococcus aureus
ComponentsYoeB
KeywordsTOXIN / toxin-antitoxin / microbial RNase / YoeB / Staphylococcus aureus
Function / homologyToxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / RNA catabolic process / endonuclease activity / negative regulation of DNA-templated transcription / Toxin YoeB
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYue, J. / Xue, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1632124 to L.N China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system.
Authors: Xue, L. / Yue, J. / Ke, J. / Khan, M.H. / Wen, W. / Sun, B. / Zhu, Z. / Niu, L.
History
DepositionAug 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: YoeB
C: YoeB
B: YoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6626
Polymers31,3743
Non-polymers2883
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, The result of size-exclusion chromatography coupled with multi-angle light scattering (SEC-MALS) experiments indicates YoeB exists as a dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-41 kcal/mol
Surface area14180 Å2
Unit cell
Length a, b, c (Å)41.467, 91.449, 154.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-256-

HOH

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Components

#1: Protein YoeB


Mass: 10457.985 Da / Num. of mol.: 3
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) / References: UniProt: Q2G286
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 25% w/v polyethylene glycol 3350, 0.1 M citric acid pH 3.5, with 1/5 volume additive of 20% 1.0 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.8→77.45 Å / Num. obs: 27885 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 22.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1096 / Rpim(I) all: 0.1142 / Rrim(I) all: 0.032 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 1.199 / Num. unique obs: 2724 / CC1/2: 0.797 / Rpim(I) all: 1.247 / Rrim(I) all: 0.339

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L8F

6l8f


Resolution: 1.8→45.72 Å / SU ML: 0.2185 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 1436 5.15 %
Rwork0.1992 26449 -
obs0.2006 27885 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 15 198 2335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342179
X-RAY DIFFRACTIONf_angle_d0.62812932
X-RAY DIFFRACTIONf_chiral_restr0.0472307
X-RAY DIFFRACTIONf_plane_restr0.0036374
X-RAY DIFFRACTIONf_dihedral_angle_d18.3836814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.31521490.27382545X-RAY DIFFRACTION98.5
1.86-1.940.2831490.23812603X-RAY DIFFRACTION99.85
1.94-2.020.24531300.19862628X-RAY DIFFRACTION99.96
2.02-2.130.24751330.1922611X-RAY DIFFRACTION100
2.13-2.260.23711570.19252621X-RAY DIFFRACTION99.96
2.26-2.440.23121460.19112642X-RAY DIFFRACTION99.96
2.44-2.680.23161490.20892605X-RAY DIFFRACTION99.17
2.68-3.070.19891380.19932676X-RAY DIFFRACTION99.93
3.07-3.870.20291270.18272720X-RAY DIFFRACTION99.96
3.87-45.720.22511580.20062798X-RAY DIFFRACTION99.93

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