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

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Basic information

Entry
Database: PDB / ID: 5cqy
TitleE. coli MazF mutant E24A in complex with MazE residues 68-82 form II
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)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.481 Å
AuthorsZorzini, V. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO) 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 1.1Jun 8, 2016Group: Database references
Revision 1.2Oct 24, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_validate_symm_contact / struct_conn
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
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

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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
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.170, 52.170, 197.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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 (E. coli) / References: UniProt: P0AE72
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 24% w/v PEG1500, 20% v/v Glycerol

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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: 2.48→44.04 Å / Num. obs: 10603 / % possible obs: 98.7 % / Redundancy: 3.68 % / Rsym value: 0.087 / Net I/σ(I): 10.83
Reflection shellResolution: 2.48→2.63 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.64 / % possible all: 98.4

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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: 2.481→44.044 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 531 5.01 %
Rwork0.1978 --
obs0.2003 10589 98.62 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.422 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.6496 Å2-0 Å2-0 Å2
2--7.6496 Å20 Å2
3----15.2992 Å2
Refinement stepCycle: LAST / Resolution: 2.481→44.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 0 11 1625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011647
X-RAY DIFFRACTIONf_angle_d1.2332241
X-RAY DIFFRACTIONf_dihedral_angle_d15.021575
X-RAY DIFFRACTIONf_chiral_restr0.084260
X-RAY DIFFRACTIONf_plane_restr0.007284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4807-2.73030.39691330.33922511X-RAY DIFFRACTION99
2.7303-3.12530.26111330.22422526X-RAY DIFFRACTION100
3.1253-3.93720.26161340.19062536X-RAY DIFFRACTION99
3.9372-44.05070.21561310.17552485X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9231-0.57540.8530.92630.3274.41450.1660.76640.2578-0.0585-0.0406-0.11140.0530.2084-0.11370.2067-0.01010.03490.3170.02770.2014.332161.07655.1575
22.74841.45550.87922.93970.85313.480.2562-0.26620.08950.2875-0.1783-0.09460.18010.3688-0.04610.2228-0.06720.02480.09940.01130.12313.155662.829624.3351
33.1159-0.76910.88170.3702-0.90172.8396-0.1358-1.08040.07310.62830.22330.4962-0.1955-0.4838-0.10120.4938-0.10370.28730.4753-0.12140.4585.33870.718814.1661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain 'A'
2X-RAY DIFFRACTION2Chain 'B'
3X-RAY DIFFRACTION3Chain 'C'

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