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- PDB-8zws: Mtb. MazF-mt3 toxin in compleex with its antitoxin fragmant -

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Basic information

Entry
Database: PDB / ID: 8zws
TitleMtb. MazF-mt3 toxin in compleex with its antitoxin fragmant
Components
  • Antitoxin MazE6
  • Endoribonuclease MazF6
KeywordsTOXIN / TA system / MazF / Mycobacterium tubercolysis / RNase
Function / homology
Function and homology information


rRNA catabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA catabolic process / RNA endonuclease activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / Arc-type ribbon-helix-helix / Ribbon-helix-helix
Similarity search - Domain/homology
Endoribonuclease MazF6 / Antitoxin MazE6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsXie, W. / Jiang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271322 China
CitationJournal: Int J Mol Sci / Year: 2024
Title: Long Dynamic beta 1-beta 2 Loops in M. tb MazF Toxins Affect the Interaction Modes and Strengths of the Toxin-Antitoxin Pairs.
Authors: Tang, Z. / Jiang, P. / Xie, W.
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoribonuclease MazF6
B: Endoribonuclease MazF6
C: Endoribonuclease MazF6
I: Antitoxin MazE6
D: Antitoxin MazE6


Theoretical massNumber of molelcules
Total (without water)46,2305
Polymers46,2305
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.740, 84.740, 101.768
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 12 or (resid 24...
d_2ens_1(chain "B" and (resid 2 through 12 or resid 24...
d_3ens_1(chain "C" and (resid 2 through 12 or (resid 24...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALASPASPAA2 - 126 - 16
d_12ARGARGLEULEUAA24 - 11428 - 118
d_21VALVALASPASPBB2 - 126 - 16
d_22ARGARGLEULEUBB24 - 11428 - 118
d_31VALVALASPASPCC2 - 126 - 16
d_32ARGARGLEULEUCC24 - 11428 - 118

NCS oper:
IDCodeMatrixVector
1given(0.138217153826, -0.990113436155, 0.0239040149935), (-0.989712602948, -0.138981065404, -0.0339591964712), (0.0369456621784, -0.0189643614176, -0.999137313407)2.29320915314, 2.06031414841, -22.4771753407
2given(-0.943432517322, -0.32893384851, 0.0416846322392), (-0.330786123747, 0.942359553432, -0.0503886137156), (-0.0227073907914, -0.0613269546003, -0.997859398434)2.78611411762, 0.522093069746, -11.2081490795

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Components

#1: Protein Endoribonuclease MazF6 / Toxin MazF6 / mRNA interferase MazF6


Mass: 12671.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Gene: mazF6, MT2046 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WII2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Protein/peptide Antitoxin MazE6


Mass: 4107.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Gene: mazE6, MT2047 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJ86
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1-2 M (NH4)2SO4, 0.1 M MES 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.27→73.39 Å / Num. obs: 6484 / % possible obs: 94.2 % / Redundancy: 14.1 % / Biso Wilson estimate: 80.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Net I/σ(I): 14.8
Reflection shellResolution: 3.27→3.46 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.909 / Num. unique obs: 791 / CC1/2: 0.885 / % possible all: 81

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.27→73.39 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 316 4.9 %
Rwork0.2395 6129 -
obs0.2409 6445 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.77 Å2
Refinement stepCycle: LAST / Resolution: 3.27→73.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 0 0 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252719
X-RAY DIFFRACTIONf_angle_d0.47853731
X-RAY DIFFRACTIONf_chiral_restr0.0436493
X-RAY DIFFRACTIONf_plane_restr0.0055478
X-RAY DIFFRACTIONf_dihedral_angle_d11.2235955
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.363790072632
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.427411682324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.27-4.120.33091520.30392806X-RAY DIFFRACTION88.25
4.12-73.390.23041640.2133323X-RAY DIFFRACTION99.71

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