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- PDB-7ewj: Toxin-antitoxin complex from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 7ewj
TitleToxin-antitoxin complex from Staphylococcus aureus
Components
  • Endoribonuclease MazF
  • PemI inhibitor
KeywordsTOXIN / Complex RNase DNA-binding protein
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / DNA binding
Similarity search - Function
SpoVT / AbrB like domain / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
Endoribonuclease MazF / PemI inhibitor
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKim, D.H. / Kang, S.M. / Lee, S.J. / Lee, B.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Role of PemI in the Staphylococcus aureus PemIK toxin-antitoxin complex: PemI controls PemK by acting as a PemK loop mimic.
Authors: Kim, D.H. / Kang, S.M. / Baek, S.M. / Yoon, H.J. / Jang, D.M. / Kim, H.S. / Lee, S.J. / Lee, B.J.
History
DepositionMay 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoribonuclease MazF
B: Endoribonuclease MazF
C: PemI inhibitor
D: Endoribonuclease MazF
E: Endoribonuclease MazF
F: PemI inhibitor
G: Endoribonuclease MazF
H: Endoribonuclease MazF
I: PemI inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,69523
Polymers92,3549
Non-polymers1,34114
Water9,278515
1
A: Endoribonuclease MazF
B: Endoribonuclease MazF
C: PemI inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,45310
Polymers30,7853
Non-polymers6687
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-91 kcal/mol
Surface area12420 Å2
MethodPISA
2
D: Endoribonuclease MazF
E: Endoribonuclease MazF
F: PemI inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1697
Polymers30,7853
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-85 kcal/mol
Surface area12310 Å2
MethodPISA
3
G: Endoribonuclease MazF
H: Endoribonuclease MazF
I: PemI inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0736
Polymers30,7853
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-91 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.509, 164.509, 232.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-340-

HOH

21I-128-

HOH

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Components

#1: Protein
Endoribonuclease MazF / Toxin MazF / mRNA interferase MazF


Mass: 13459.659 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SACH_a18 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L7PFJ6
#2: Protein/peptide PemI inhibitor / PemI inhibitor


Mass: 3865.264 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SACH_a19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L7PH55
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.39 Å3/Da / Density % sol: 71.97 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0 M ammonium sulfate, 100 mM CAPS/Sodium hydroxide, pH 10.5, 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 205519 / % possible obs: 99.8 % / Redundancy: 7.12 % / CC1/2: 1 / Net I/σ(I): 19.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 7.17 % / Num. unique obs: 32910 / CC1/2: 0.789 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→38.77 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 3826 1.86 %
Rwork0.1877 --
obs0.1883 205486 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 0 71 515 6861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186430
X-RAY DIFFRACTIONf_angle_d1.6498685
X-RAY DIFFRACTIONf_dihedral_angle_d14.406842
X-RAY DIFFRACTIONf_chiral_restr0.097989
X-RAY DIFFRACTIONf_plane_restr0.0111091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.31421270.28337160X-RAY DIFFRACTION95
2.02-2.050.29781410.2597470X-RAY DIFFRACTION100
2.05-2.080.26711340.24167556X-RAY DIFFRACTION100
2.08-2.110.26141480.22357472X-RAY DIFFRACTION100
2.11-2.140.28051370.2267456X-RAY DIFFRACTION100
2.14-2.170.23561500.22017453X-RAY DIFFRACTION100
2.17-2.210.24881410.21867455X-RAY DIFFRACTION100
2.21-2.250.23881450.20877473X-RAY DIFFRACTION100
2.25-2.290.23621480.21357498X-RAY DIFFRACTION100
2.29-2.330.24681470.20167447X-RAY DIFFRACTION100
2.33-2.380.28011420.20287509X-RAY DIFFRACTION100
2.38-2.430.2171530.1927463X-RAY DIFFRACTION100
2.43-2.490.25131410.19877520X-RAY DIFFRACTION100
2.49-2.550.2751410.19587398X-RAY DIFFRACTION100
2.55-2.620.24741440.20487508X-RAY DIFFRACTION100
2.62-2.70.26181430.19787516X-RAY DIFFRACTION100
2.7-2.780.22571380.19897500X-RAY DIFFRACTION100
2.78-2.880.2481410.20247465X-RAY DIFFRACTION100
2.88-30.19661360.19447499X-RAY DIFFRACTION100
3-3.140.24171390.19277461X-RAY DIFFRACTION100
3.14-3.30.25111470.18687468X-RAY DIFFRACTION100
3.3-3.510.18931440.18527503X-RAY DIFFRACTION100
3.51-3.780.21951330.16477449X-RAY DIFFRACTION100
3.78-4.160.20061320.15777491X-RAY DIFFRACTION100
4.16-4.760.14891380.1437488X-RAY DIFFRACTION100
4.76-5.990.22241450.18827507X-RAY DIFFRACTION100
5.99-38.770.19771510.21027475X-RAY DIFFRACTION100

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