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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 / positive regulation of programmed cell death / regulation of growth / 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 / positive regulation of programmed cell death / regulation of growth / 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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