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- PDB-5ckh: E. coli MazF E24A form IIb -

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Basic information

Entry
Database: PDB / ID: 5ckh
TitleE. coli MazF E24A form IIb
ComponentsEndoribonuclease MazF
KeywordsHYDROLASE / Toxin-Antitoxin / mRNA interferase / ribonuclease / persistence / bacterial stress response
Function / homology
Function and homology information


toxin-antitoxin complex / rRNA catabolic process / quorum sensing / 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 / rRNA catabolic process / quorum sensing / 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 / protein-containing complex binding / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Endoribonuclease toxin MazF
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.449 Å
AuthorsZorzini, V. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO) Belgium
Biostruct-X Belgium
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF.
Authors: Zorzini, V. / Mernik, A. / Lah, J. / Sterckx, Y.G. / De Jonge, N. / Garcia-Pino, A. / De Greve, H. / Versees, W. / Loris, R.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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
A: Endoribonuclease MazF
B: Endoribonuclease MazF


Theoretical massNumber of molelcules
Total (without water)26,1662
Polymers26,1662
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-15 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.199, 64.199, 224.535
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 13083.104 Da / Num. of mol.: 2 / Mutation: E24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mazF, chpA, chpAK, b2782, JW2753 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AE70, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M MOPS/Na Hepes pH 7.5, 0.02M of each a.a.,12.5% PEG1000, 12,.5% PEG3350, 12.5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.449→44.63 Å / Num. all: 10883 / Num. obs: 10883 / % possible obs: 99.5 % / Redundancy: 10.1 % / Rsym value: 0.125 / Net I/σ(I): 20.54
Reflection shellResolution: 2.449→2.54 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1581 / Rsym value: 0.599 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UB4

1ub4


Resolution: 2.449→44.631 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 523 4.82 %
Rwork0.2089 --
obs0.2111 10843 99.86 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.251 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6445 Å2-0 Å2-0 Å2
2--4.6445 Å20 Å2
3----9.289 Å2
Refinement stepCycle: LAST / Resolution: 2.449→44.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 0 48 1665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081677
X-RAY DIFFRACTIONf_angle_d1.0832280
X-RAY DIFFRACTIONf_dihedral_angle_d13.898620
X-RAY DIFFRACTIONf_chiral_restr0.067263
X-RAY DIFFRACTIONf_plane_restr0.005290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.449-2.69550.32261430.24032480X-RAY DIFFRACTION100
2.6955-3.08540.29161300.20532510X-RAY DIFFRACTION100
3.0854-3.88690.27671240.20282556X-RAY DIFFRACTION100
3.8869-44.63870.20611260.2062774X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9431-0.02781.22831.13690.30961.88740.02470.26340.0796-0.16060.00440.0083-0.06090.28780.08210.07140.007-0.03430.2573-0.02470.10754.7291-23.3402-19.9341
22.89881.23980.51591.0455-0.23991.41260.0024-0.20510.17690.0648-0.03010.1306-0.1336-0.09970.00760.04920.0113-0.03360.1947-0.03450.11858.5962-20.65071.5292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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