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- PDB-5xe3: Endoribonuclease in complex with its cognate antitoxin from Mycob... -

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Basic information

Entry
Database: PDB / ID: 5xe3
TitleEndoribonuclease in complex with its cognate antitoxin from Mycobacterial species
Components
  • Endoribonuclease MazF4
  • Probable antitoxin MazE4
KeywordsHYDROLASE/ANTITOXIN / endonuclease / HYDROLASE-ANTITOXIN complex
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / enzyme inhibitor activity / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA 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 MazF4 / Probable antitoxin MazE4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAhn, D.-H. / Lee, K.-Y. / Lee, S.J. / Yoon, H.J. / Kim, S.-J. / Lee, B.-J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF)2015R1A2A1A05001894 Korea, Republic Of
National Research Foundation of Korea (NRF)2014K1A3A1A19067618 Korea, Republic Of
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of the MazEF4 toxin-antitoxin pair in Mycobacterium tuberculosis provide evidence for a unique extracellular death factor.
Authors: Ahn, D.H. / Lee, K.Y. / Lee, S.J. / Park, S.J. / Yoon, H.J. / Kim, S.J. / Lee, B.J.
History
DepositionMar 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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
C: Endoribonuclease MazF4
D: Endoribonuclease MazF4
F: Probable antitoxin MazE4
A: Endoribonuclease MazF4
B: Endoribonuclease MazF4
E: Probable antitoxin MazE4


Theoretical massNumber of molelcules
Total (without water)65,2116
Polymers65,2116
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-36 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.473, 70.018, 76.754
Angle α, β, γ (deg.)90.000, 113.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endoribonuclease MazF4 / Toxin MazF4 / mRNA interferase MazF-mt7


Mass: 11697.274 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazF4, mazF-mt7, Rv1495, MTCY277.17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WII5, Hydrolases; Acting on ester bonds
#2: Protein Probable antitoxin MazE4


Mass: 9211.135 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazE4, mazE-mt7, Rv1494, MTCY277.16 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WJ91
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.0, 20% (w/v) polyethylene glycol 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 23785 / % possible obs: 95.21 % / Redundancy: 4 % / Net I/σ(I): 30.21

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE5

3se5


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.27 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.434 / ESU R Free: 0.274
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 1268 5.1 %RANDOM
Rwork0.2117 ---
obs0.2145 23785 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.57 Å2 / Biso mean: 44.244 Å2 / Biso min: 22.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.04 Å2
2--0.07 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 0 70 4444
Biso mean---38.39 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194462
X-RAY DIFFRACTIONr_bond_other_d0.0020.024248
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9596088
X-RAY DIFFRACTIONr_angle_other_deg1.00639702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25923.301206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51915654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9221546
X-RAY DIFFRACTIONr_chiral_restr0.0880.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021034
LS refinement shellResolution: 2.301→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 84 -
Rwork0.293 1430 -
all-1514 -
obs--78.65 %

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