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- PDB-6l8f: Crystal structure of heterotetrameric complex of YoeB-YefM toxin-... -

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Basic information

Entry
Database: PDB / ID: 6l8f
TitleCrystal structure of heterotetrameric complex of YoeB-YefM toxin-antitoxin from Staphylococcus aureus.
Components
  • Antitoxin
  • YoeB
KeywordsTOXIN/ANTITOXIN / toxin-antitoxin / microbial RNase / YoeB / Staphylococcus aureus / TOXIN / TOXIN-ANTITOXIN complex
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: 2.4 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
D: YoeB
B: Antitoxin
C: YoeB
A: Antitoxin
H: YoeB
F: Antitoxin
G: YoeB
E: Antitoxin


Theoretical massNumber of molelcules
Total (without water)82,9188
Polymers82,9188
Non-polymers00
Water2,126118
1
D: YoeB
B: Antitoxin
C: YoeB
A: Antitoxin


Theoretical massNumber of molelcules
Total (without water)41,4594
Polymers41,4594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-56 kcal/mol
Surface area16520 Å2
MethodPISA
2
H: YoeB
F: Antitoxin
G: YoeB
E: Antitoxin


Theoretical massNumber of molelcules
Total (without water)41,4594
Polymers41,4594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-56 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.438, 104.438, 172.586
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein
YoeB


Mass: 10457.985 Da / Num. of mol.: 4
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
#2: Protein
Antitoxin


Mass: 10271.464 Da / Num. of mol.: 4
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_02692 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G285
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.41 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.07 M Citric acid, 0.03 M BIS-TRIS propane, pH 3.4, 16% 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: BL18U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 41475 / % possible obs: 99.9 % / Redundancy: 20.5 % / Biso Wilson estimate: 40.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.039 / Rrim(I) all: 0.179 / Net I/σ(I): 15.5
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.439 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4340 / CC1/2: 0.827 / Rpim(I) all: 0.341 / Rrim(I) all: 1.48

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A6Q

2a6q


Resolution: 2.4→62.43 Å / SU ML: 0.2584 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3146
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2234 2081 5.03 %
Rwork0.1895 39324 -
obs0.1912 41405 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.31 Å2
Refinement stepCycle: LAST / Resolution: 2.4→62.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 0 118 5674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065638
X-RAY DIFFRACTIONf_angle_d0.83547586
X-RAY DIFFRACTIONf_chiral_restr0.0518842
X-RAY DIFFRACTIONf_plane_restr0.0049980
X-RAY DIFFRACTIONf_dihedral_angle_d21.56252174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.31611400.23822582X-RAY DIFFRACTION99.6
2.46-2.520.27831330.22732641X-RAY DIFFRACTION100
2.52-2.590.27111380.2262610X-RAY DIFFRACTION99.93
2.59-2.660.28641430.22052615X-RAY DIFFRACTION100
2.66-2.750.27831220.21822631X-RAY DIFFRACTION100
2.75-2.850.22161430.19842623X-RAY DIFFRACTION100
2.85-2.960.23521250.19982622X-RAY DIFFRACTION100
2.96-3.10.25121410.20262598X-RAY DIFFRACTION100
3.1-3.260.2351580.19322632X-RAY DIFFRACTION99.96
3.26-3.470.21881490.18772593X-RAY DIFFRACTION99.96
3.47-3.730.22481520.1832626X-RAY DIFFRACTION100
3.73-4.110.19471190.17452636X-RAY DIFFRACTION100
4.11-4.70.1821260.1592646X-RAY DIFFRACTION100
4.7-5.920.20731440.18262625X-RAY DIFFRACTION100
5.93-62.430.21571480.19222644X-RAY DIFFRACTION99.54

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