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- PDB-5xe2: Endoribonuclease from Mycobacterial species -

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Basic information

Entry
Database: PDB / ID: 5xe2
TitleEndoribonuclease from Mycobacterial species
ComponentsEndoribonuclease MazF4
KeywordsHYDROLASE / endonuclease
Function / homology
Function and homology information


negative regulation of DNA topoisomerase (ATP-hydrolyzing) activity / rRNA catabolic process / mRNA catabolic process / 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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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

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Assembly

Deposited unit
A: Endoribonuclease MazF4


Theoretical massNumber of molelcules
Total (without water)11,6971
Polymers11,6971
Non-polymers00
Water1,06359
1
A: Endoribonuclease MazF4

A: Endoribonuclease MazF4


Theoretical massNumber of molelcules
Total (without water)23,3952
Polymers23,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1840 Å2
ΔGint-10 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.475, 65.548, 57.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 11697.274 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 0.2M sodium malonate at pH 7.0 and 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.01→30 Å / Num. obs: 7261 / % possible obs: 97.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.054 / Rrim(I) all: 0.157 / Χ2: 1.923 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.87-1.97.70.7340.8840.2730.7870.79992.5
1.9-1.9480.6640.890.2410.7090.98693.9
1.94-1.9780.5440.9370.1970.5811.02595.5
1.97-2.0180.5520.8970.2040.591.11197.6
2.01-2.067.90.440.9340.1650.4711.29797.5
2.06-2.117.80.4170.9480.1540.4461.56498.3
2.11-2.167.40.3840.9350.1450.4131.76497.8
2.16-2.227.40.3560.9630.1350.3821.81996.8
2.22-2.288.30.3390.9720.1210.3611.87798
2.28-2.368.60.2910.9790.1050.311.85596.9
2.36-2.448.30.2730.9740.0980.2912.05698.1
2.44-2.548.20.2480.9850.0910.2651.94998.6
2.54-2.6580.2070.9890.0770.2212.05997.8
2.65-2.797.10.1980.9830.0770.2132.60398.6
2.79-2.977.60.1750.9850.0670.1882.85797.6
2.97-3.28.20.1430.9870.0510.1522.47498.9
3.2-3.5280.1190.9940.0440.1282.82599
3.52-4.037.20.1030.9910.040.1112.82399.2
4.03-5.077.90.0860.9940.0310.0922.58699.2
5.07-307.70.0770.9940.0290.0821.9797.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XE3

5xe3


Resolution: 2.01→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.373 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.171
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 307 4.8 %RANDOM
Rwork0.2037 ---
obs0.2046 6119 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 57.44 Å2 / Biso mean: 23.868 Å2 / Biso min: 12.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.13 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 2.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 0 59 860
Biso mean---33.14 -
Num. residues----104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02818
X-RAY DIFFRACTIONr_bond_other_d0.0030.02787
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9621120
X-RAY DIFFRACTIONr_angle_other_deg0.87431802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31323.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88215127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.051157
X-RAY DIFFRACTIONr_chiral_restr0.060.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02179
LS refinement shellResolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 21 -
Rwork0.217 412 -
all-433 -
obs--89.83 %

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