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- PDB-7v5z: Crystal structure of heterotetrameric complex of Sa2YoeB-Sa2YefM ... -

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Basic information

Entry
Database: PDB / ID: 7v5z
TitleCrystal structure of heterotetrameric complex of Sa2YoeB-Sa2YefM toxin-antitoxin from Staphylococcus aureus
Components
  • Antitoxin
  • Putative mRNA interferase YoeB
KeywordsANTITOXIN / TOXIN/ANTITOXIN
Function / homology
Function and homology information


global gene silencing by mRNA cleavage / 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 speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsXue, L. / Khan, M.H. / Yue, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The two paralogous copies of the YoeB-YefM toxin-antitoxin module in Staphylococcus aureus differ in DNA binding and recognition patterns.
Authors: Xue, L. / Khan, M.H. / Yue, J. / Zhu, Z. / Niu, L.
History
DepositionAug 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin
B: Antitoxin
C: Putative mRNA interferase YoeB
D: Putative mRNA interferase YoeB


Theoretical massNumber of molelcules
Total (without water)40,9084
Polymers40,9084
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-35 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.694, 92.243, 108.813
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 Antitoxin


Mass: 9783.692 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_02757 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FVF7
#2: Protein Putative mRNA interferase YoeB / Toxin YoeB


Mass: 10670.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_02756 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FVF8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Succinic acid pH 7.0, 20% w/v Polyethylene glycol 3350

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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: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 23229 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 29.57 Å2 / CC1/2: 0.991 / Net I/σ(I): 12.1
Reflection shellResolution: 1.99→2.03 Å / Redundancy: 10.4 % / Num. unique obs: 1152 / CC1/2: 0.768 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V5Y

7v5y


Resolution: 1.99→33.76 Å / SU ML: 0.2008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2176 1104 4.77 %
Rwork0.1725 22038 -
obs0.1747 23142 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.44 Å2
Refinement stepCycle: LAST / Resolution: 1.99→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 0 240 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692916
X-RAY DIFFRACTIONf_angle_d0.88573938
X-RAY DIFFRACTIONf_chiral_restr0.0553434
X-RAY DIFFRACTIONf_plane_restr0.0046504
X-RAY DIFFRACTIONf_dihedral_angle_d7.09571788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.090.31641220.22922675X-RAY DIFFRACTION97.97
2.09-2.20.26011530.1862705X-RAY DIFFRACTION99.97
2.2-2.330.24291450.18012737X-RAY DIFFRACTION100
2.33-2.510.24951230.18052738X-RAY DIFFRACTION99.83
2.51-2.770.2531430.18212720X-RAY DIFFRACTION99.9
2.77-3.170.21751400.18252747X-RAY DIFFRACTION99.69
3.17-3.990.19541300.15812813X-RAY DIFFRACTION99.9
3.99-33.760.18741480.16012903X-RAY DIFFRACTION98.36

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