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- PDB-4me7: Crystal structure of Bacillus subtilis toxin MazF in complex with... -

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Basic information

Entry
Database: PDB / ID: 4me7
TitleCrystal structure of Bacillus subtilis toxin MazF in complex with cognate antitoxin MazE
Components
  • Antitoxin EndoAI
  • mRNA interferase EndoA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Toxin-antitoxin system / MazE-MazF / Stress response / mRNA clevage / MazE / Antitoxin / MazF / mRNA interferase / EndoA / YdcE / HYDROLASE-HYDROLASE INHIBITOR complex
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 / RNA binding / identical protein binding
Similarity search - Function
SH3 type barrels. - #110 / 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 / Met repressor-like / Plasmid maintenance toxin/Cell growth inhibitor / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix ...SH3 type barrels. - #110 / 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 / Met repressor-like / Plasmid maintenance toxin/Cell growth inhibitor / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / SH3 type barrels. / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Antitoxin EndoAI / Endoribonuclease EndoA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.918 Å
AuthorsSimanshu, D.K. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2013
Title: Structural Basis of mRNA Recognition and Cleavage by Toxin MazF and Its Regulation by Antitoxin MazE in Bacillus subtilis.
Authors: Simanshu, D.K. / Yamaguchi, Y. / Park, J.H. / Inouye, M. / Patel, D.J.
History
DepositionAug 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 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: mRNA interferase EndoA
B: mRNA interferase EndoA
C: mRNA interferase EndoA
D: mRNA interferase EndoA
E: Antitoxin EndoAI
F: Antitoxin EndoAI


Theoretical massNumber of molelcules
Total (without water)74,4016
Polymers74,4016
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-75 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.503, 91.618, 104.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and (resseq 1:16 or resseq 24:113 )
21chain D and (resseq 1:16 or resseq 24:113 )
31chain C and (resseq 1:16 or resseq 24:113 )
12chain E and (resseq 7:83 )
22chain F and (resseq 7:83 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'B' and (resseq 1:16 or resseq 24:113 )B1 - 16
121chain 'B' and (resseq 1:16 or resseq 24:113 )B24 - 113
211chain 'D' and (resseq 1:16 or resseq 24:113 )D1 - 16
221chain 'D' and (resseq 1:16 or resseq 24:113 )D24 - 113
311chain 'C' and (resseq 1:16 or resseq 24:113 )C1 - 16
321chain 'C' and (resseq 1:16 or resseq 24:113 )C24 - 113
112chain 'E' and (resseq 7:83 )E7 - 83
212chain 'F' and (resseq 7:83 )F7 - 83

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.985198, -0.116141, 0.126076), (-0.135202, -0.074343, 0.988025), (-0.105378, -0.990447, -0.088945)-47.304298, 41.194099, 2.95518
2given(-0.999861, -0.002911, -0.016397), (0.000494, -0.989356, 0.145511), (-0.016646, 0.145483, 0.989221)-40.903702, 45.1427, -3.10509
3given(-0.999882, -0.006747, -0.013781), (0.004286, -0.985201, 0.171352), (-0.014733, 0.171273, 0.985113)-40.610401, 45.611, -4.18004

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Components

#1: Protein
mRNA interferase EndoA / Endoribonuclease EndoA / Toxin EndoA / mRNA interferase MazF-bs / MazF-bs


Mass: 13134.627 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU04660, mazF, ndoA, ydcE / Plasmid: pRSF-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P96622, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin EndoAI / Antitoxin MazE-bs / MazE-bs / EndoA inhibitor


Mass: 10931.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MazE and MazF proteins were co-expressed in E. coli.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU04650, mazE, ndoAI / Plasmid: pRSF-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P96621
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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 Matthews: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium chloride, 0.1 M Bis-Tris pH 6.5 and 3% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Number: 95544 / Rmerge(I) obs: 0.102 / Χ2: 3.15 / D res high: 2.92 Å / D res low: 30 Å / Num. obs: 17173 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.273099.210.07911.7775
4.996.2799.910.1046.1225.5
4.364.9999.910.0874.0815.6
3.964.3610010.0982.9485.7
3.683.9610010.1312.0695.8
3.463.6810010.1621.4515.8
3.293.4610010.2241.135.9
3.153.2999.910.3430.8685.9
3.023.1599.310.4740.7135.5
2.923.0296.610.6440.6495
ReflectionResolution: 2.918→45.33 Å / Num. obs: 17226 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 90.67 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 31.6
Reflection shellResolution: 2.918→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.85 / Num. unique all: 1648 / % possible all: 97.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 4MDX

4mdx


Resolution: 2.918→45.33 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6855 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2989 1714 10 %Random
Rwork0.253 ---
obs0.2574 17139 97.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.84 Å2 / Biso mean: 60.5104 Å2 / Biso min: 21.34 Å2
Refinement stepCycle: LAST / Resolution: 2.918→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4609 0 0 30 4639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074653
X-RAY DIFFRACTIONf_angle_d1.0856266
X-RAY DIFFRACTIONf_chiral_restr0.067751
X-RAY DIFFRACTIONf_plane_restr0.003806
X-RAY DIFFRACTIONf_dihedral_angle_d14.6761796
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B798X-RAY DIFFRACTIONTORSIONAL0.076
12D798X-RAY DIFFRACTIONTORSIONAL0.076
13C838X-RAY DIFFRACTIONTORSIONAL0.065
21E614X-RAY DIFFRACTIONTORSIONAL0.063
22F614X-RAY DIFFRACTIONTORSIONAL0.063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9179-3.00370.44411090.3565987109677
3.0037-3.10070.37291410.35581263140498
3.1007-3.21150.38761440.324912851429100
3.2115-3.340.36051430.29712911434100
3.34-3.4920.32511450.277113021447100
3.492-3.6760.29321450.268213071452100
3.676-3.90620.34481440.257912981442100
3.9062-4.20760.29311460.240213141460100
4.2076-4.63060.27221450.205813101455100
4.6306-5.29980.26771480.221513361484100
5.2998-6.67380.30571510.267413491500100
6.6738-45.33870.27191530.24831383153698
Refinement TLS params.Method: refined / Origin x: -20.2013 Å / Origin y: 21.1067 Å / Origin z: -24.0215 Å
111213212223313233
T0.3477 Å20.0916 Å2-0.0047 Å2-0.314 Å20.0566 Å2--0.2255 Å2
L3.3098 °21.0549 °2-0.2562 °2-0.9715 °2-0.2527 °2--0.5537 °2
S0.0271 Å °0.6349 Å °0.0141 Å °-0.0248 Å °-0.0296 Å °-0.0319 Å °0.0874 Å °0.0156 Å °0.0411 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 114
2X-RAY DIFFRACTION1allB1 - 114
3X-RAY DIFFRACTION1allC1 - 114
4X-RAY DIFFRACTION1allD1 - 114
5X-RAY DIFFRACTION1allE6 - 83
6X-RAY DIFFRACTION1allF7 - 85
7X-RAY DIFFRACTION1allC - A1 - 205

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