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- PDB-6l8e: Crystal structure of heterohexameric YoeB-YefM complex bound to 2... -

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Basic information

Entry
Database: PDB / ID: 6l8e
TitleCrystal structure of heterohexameric YoeB-YefM complex bound to 26bp-DNA
Components
  • (DNA (26-mer)) x 2
  • YefM Antitoxin
  • YoeB toxin
KeywordsANTITOXIN/TOXIN/DNA / toxin-antitoxin / microbial RNase / YoeB / Staphylococcus aureus / TOXIN / ANTITOXIN-TOXIN-DNA complex
Function / homology
Function and homology information


RNA catabolic process / endonuclease activity / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / 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
DNA / DNA (> 10) / Antitoxin / Toxin YoeB
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
DepositionNov 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: YefM Antitoxin
B: YefM Antitoxin
C: YefM Antitoxin
D: YefM Antitoxin
E: YoeB toxin
F: YoeB toxin
G: DNA (26-mer)
H: DNA (26-mer)
I: YefM Antitoxin
J: YefM Antitoxin
K: YefM Antitoxin
L: YefM Antitoxin
M: YoeB toxin
N: YoeB toxin
O: DNA (26-mer)
P: DNA (26-mer)


Theoretical massNumber of molelcules
Total (without water)149,30916
Polymers149,30916
Non-polymers00
Water5,675315
1
A: YefM Antitoxin
B: YefM Antitoxin
C: YefM Antitoxin
D: YefM Antitoxin
E: YoeB toxin
F: YoeB toxin
G: DNA (26-mer)
H: DNA (26-mer)


Theoretical massNumber of molelcules
Total (without water)74,6558
Polymers74,6558
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20990 Å2
ΔGint-125 kcal/mol
Surface area24760 Å2
MethodPISA
2
I: YefM Antitoxin
J: YefM Antitoxin
K: YefM Antitoxin
L: YefM Antitoxin
M: YoeB toxin
N: YoeB toxin
O: DNA (26-mer)
P: DNA (26-mer)


Theoretical massNumber of molelcules
Total (without water)74,6558
Polymers74,6558
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21280 Å2
ΔGint-126 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.352, 151.352, 183.778
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
YefM Antitoxin


Mass: 9442.584 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus 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 toxin


Mass: 10457.985 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus 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: DNA chain DNA (26-mer)


Mass: 8006.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (26-mer)


Mass: 7962.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.54 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→92.48 Å / Num. obs: 89409 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.03 / Rrim(I) all: 0.083 / Net I/σ(I): 17.4
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4434 / CC1/2: 0.791 / Rpim(I) all: 0.403 / Rrim(I) all: 1.147

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A6Q

2a6q


Resolution: 2.35→53.51 Å / SU ML: 0.2967 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2225 4531 5.07 %
Rwork0.1971 84765 -
obs0.1985 89296 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.54 Å2
Refinement stepCycle: LAST / Resolution: 2.35→53.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7305 1855 0 315 9475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00379476
X-RAY DIFFRACTIONf_angle_d0.658113162
X-RAY DIFFRACTIONf_chiral_restr0.04241494
X-RAY DIFFRACTIONf_plane_restr0.00271369
X-RAY DIFFRACTIONf_dihedral_angle_d25.55233732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.370.3181310.282732X-RAY DIFFRACTION97.31
2.37-2.40.30481680.27052785X-RAY DIFFRACTION100
2.4-2.430.36331500.29032783X-RAY DIFFRACTION99.86
2.43-2.460.31241300.26732791X-RAY DIFFRACTION100
2.46-2.490.2741430.262800X-RAY DIFFRACTION100
2.49-2.530.31771280.25492831X-RAY DIFFRACTION100
2.53-2.560.25241520.25242809X-RAY DIFFRACTION100
2.56-2.60.32661620.25692769X-RAY DIFFRACTION100
2.6-2.640.28771240.25882834X-RAY DIFFRACTION99.86
2.64-2.690.34271390.26182793X-RAY DIFFRACTION99.97
2.69-2.730.3221540.24992787X-RAY DIFFRACTION99.9
2.73-2.780.27281470.24082795X-RAY DIFFRACTION100
2.78-2.840.23471670.22542811X-RAY DIFFRACTION99.97
2.84-2.890.23081660.22142773X-RAY DIFFRACTION99.97
2.89-2.960.2441650.22142797X-RAY DIFFRACTION100
2.96-3.020.27851420.2242828X-RAY DIFFRACTION99.87
3.02-3.10.25651540.23562818X-RAY DIFFRACTION100
3.1-3.180.26631580.22592797X-RAY DIFFRACTION99.93
3.18-3.280.22871610.22872810X-RAY DIFFRACTION100
3.28-3.380.2621270.21772836X-RAY DIFFRACTION99.97
3.38-3.50.23271650.20672820X-RAY DIFFRACTION99.9
3.5-3.640.21521470.19382829X-RAY DIFFRACTION100
3.64-3.810.22661530.18852846X-RAY DIFFRACTION99.73
3.81-4.010.22351560.19072831X-RAY DIFFRACTION99.7
4.01-4.260.20191450.17452854X-RAY DIFFRACTION99.8
4.26-4.590.18581420.1552872X-RAY DIFFRACTION99.7
4.59-5.050.16381540.14932875X-RAY DIFFRACTION99.7
5.05-5.780.19841530.1652885X-RAY DIFFRACTION99.77
5.78-7.280.20451750.19232915X-RAY DIFFRACTION99.74
7.28-100.15331730.15333059X-RAY DIFFRACTION98.93

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