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- PDB-9pme: Crystallographic structure of MazF-E24A toxin bound to SamF -

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Basic information

Entry
Database: PDB / ID: 9pme
TitleCrystallographic structure of MazF-E24A toxin bound to SamF
Components
  • Endoribonuclease toxin MazF
  • peptide SER-HIS-LEU-PHE-TRP-ALA-GLN-PHE-ASP-GLU-TYR-PHE
KeywordsTOXIN / MazF / toxin-antitoxin system / MazF inhibitor
Function / homology
Function and homology information


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 ...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 / 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
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 toxin MazF
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPizzolato-Cezar, L.R. / Nascimento, A.F.Z. / Machini, M.T. / Salinas, R.K.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/10577-0 Brazil
Sao Paulo Research Foundation (FAPESP)2022/01825-2 Brazil
CitationJournal: J.Med.Chem. / Year: 2025
Title: Development of a Potent and Functional In Vivo Peptide Competitive Inhibitor for the Toxin MazF.
Authors: Pizzolato-Cezar, L.R. / Vitale, P.M. / Liria, C.W. / Pineda, M.A.R. / Lacerda, C.D. / Marana, S.R. / Nascimento, A.F.Z. / Sassonia, R.C. / Sgro, G.G. / Salinas, R.K. / Machini, M.T.
History
DepositionJul 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Source and taxonomy / Category: citation / citation_author / pdbx_entity_src_syn / Item: _pdbx_entity_src_syn.ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoribonuclease toxin MazF
B: peptide SER-HIS-LEU-PHE-TRP-ALA-GLN-PHE-ASP-GLU-TYR-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6923
Polymers13,6692
Non-polymers231
Water1,58588
1
A: Endoribonuclease toxin MazF
B: peptide SER-HIS-LEU-PHE-TRP-ALA-GLN-PHE-ASP-GLU-TYR-PHE
hetero molecules

A: Endoribonuclease toxin MazF
B: peptide SER-HIS-LEU-PHE-TRP-ALA-GLN-PHE-ASP-GLU-TYR-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3836
Polymers27,3374
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)59.222, 59.222, 66.432
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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


Mass: 12053.987 Da / Num. of mol.: 1 / Mutation: E24A
Source method: isolated from a genetically manipulated source
Details: This is the mutant E24A The first amino acid is a glycine that comes from the plasmid
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mazF, chpA, chpAK, b2782, JW2753 / Plasmid: pET-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL
References: UniProt: P0AE70, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Protein/peptide peptide SER-HIS-LEU-PHE-TRP-ALA-GLN-PHE-ASP-GLU-TYR-PHE


Mass: 1614.756 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide N-terminus was acetylated and C-terminus was amidated
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 Matthews: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M sodium cacodylate pH 6.5, 1.26 M (NH4)2SO4. / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2025
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.52→51.29 Å / Num. obs: 21219 / % possible obs: 99.53 % / Redundancy: 17.6 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.09505 / Net I/σ(I): 14.23
Reflection shellResolution: 1.52→1.59 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2539 / Rrim(I) all: 2.048 / % possible all: 96.67

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSBUILT=20230630data reduction
XDSBUILT=20230630data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→51.29 Å / SU ML: 0.2081 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2025 1061 5.01 %
Rwork0.1697 20133 -
obs0.1714 21194 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.91 Å2
Refinement stepCycle: LAST / Resolution: 1.52→51.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 5 88 983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0201953
X-RAY DIFFRACTIONf_angle_d1.59371306
X-RAY DIFFRACTIONf_chiral_restr0.0911148
X-RAY DIFFRACTIONf_plane_restr0.0219165
X-RAY DIFFRACTIONf_dihedral_angle_d13.6693352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.590.34481270.30172400X-RAY DIFFRACTION96.67
1.59-1.670.30071300.23092469X-RAY DIFFRACTION99.96
1.67-1.770.26651320.19632506X-RAY DIFFRACTION99.92
1.78-1.910.22471320.15872519X-RAY DIFFRACTION99.85
1.91-2.10.21581320.1512493X-RAY DIFFRACTION99.89
2.1-2.410.231330.15352526X-RAY DIFFRACTION99.92
2.41-3.030.19141340.17032553X-RAY DIFFRACTION99.96
3.04-51.290.17751410.16582667X-RAY DIFFRACTION99.96

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