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- PDB-5cqx: E. coli MazF mutant E24A in complex with MazE residues 68-82 form I -

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Basic information

Entry
Database: PDB / ID: 5cqx
TitleE. coli MazF mutant E24A in complex with MazE residues 68-82 form I
Components
  • Antitoxin MazE
  • Endoribonuclease MazF
KeywordsHYDROLASE / Toxin-Antitoxin / mRNA interferase / ribonuclease / persistence / bacterial stress response
Function / homology
Function and homology information


toxin sequestering activity / toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / regulation of growth / positive regulation of programmed cell death / mRNA catabolic process / RNA endonuclease activity ...toxin sequestering activity / toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / regulation of growth / positive regulation of programmed cell death / mRNA catabolic process / RNA endonuclease activity / molecular function activator activity / negative regulation of cell growth / regulation of translation / double-stranded DNA binding / defense response to virus / regulation of DNA-templated transcription / protein-containing complex binding / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding
Similarity search - Function
: / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SH3 type barrels. - #110 / 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 ...: / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SH3 type barrels. - #110 / 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 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Endoribonuclease toxin MazF / Antitoxin MazE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZorzini, V. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek-Vlaanderen Belgium
Biostruct-X Belgium
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF.
Authors: Zorzini, V. / Mernik, A. / Lah, J. / Sterckx, Y.G. / De Jonge, N. / Garcia-Pino, A. / De Greve, H. / Versees, W. / Loris, R.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Antitoxin MazE


Theoretical massNumber of molelcules
Total (without water)28,0513
Polymers28,0513
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-26 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.760, 32.250, 86.260
Angle α, β, γ (deg.)90.00, 97.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-250-

HOH

21B-290-

HOH

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Components

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


Mass: 13083.104 Da / Num. of mol.: 2 / Mutation: E24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mazF, chpA, chpAK, b2782, JW2753 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AE70, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Protein/peptide Antitoxin MazE


Mass: 1885.016 Da / Num. of mol.: 1 / Fragment: UNP residues 68-82 / Source method: obtained synthetically / Details: Peptide / Source: (synth.) Escherichia coli K-12 (bacteria) / References: UniProt: P0AE72
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 % sol: 27.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Magnesium Chloride, 0.1M Sodium Cacodylate pH6.5, 50% v/v PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.63→42.74 Å / Num. obs: 22847 / % possible obs: 95.9 % / Redundancy: 3.62 % / Rsym value: 0.1 / Net I/σ(I): 11.1
Reflection shellResolution: 1.63→1.73 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.11 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UB4

1ub4


Resolution: 1.63→42.745 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 1142 5 %
Rwork0.1745 --
obs0.1776 22828 95.87 %
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.416 Å2 / ksol: 0.393 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1303 Å20 Å2-2.2149 Å2
2--2.6197 Å2-0 Å2
3---0.5106 Å2
Refinement stepCycle: LAST / Resolution: 1.63→42.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 185 1992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081924
X-RAY DIFFRACTIONf_angle_d1.0512627
X-RAY DIFFRACTIONf_dihedral_angle_d11.721699
X-RAY DIFFRACTIONf_chiral_restr0.072298
X-RAY DIFFRACTIONf_plane_restr0.005331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6298-1.70390.52241310.48542494X-RAY DIFFRACTION89
1.7039-1.79380.38011410.27822669X-RAY DIFFRACTION95
1.7938-1.90620.23521420.18272697X-RAY DIFFRACTION96
1.9062-2.05330.24121410.15992689X-RAY DIFFRACTION97
2.0533-2.260.25791440.16082729X-RAY DIFFRACTION97
2.26-2.58690.22821450.15132757X-RAY DIFFRACTION97
2.5869-3.25910.21991470.15782794X-RAY DIFFRACTION98
3.2591-42.75980.1941510.16072857X-RAY DIFFRACTION98

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