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- PDB-5ckf: E. coli MazF E24A form I -

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Basic information

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


toxin-antitoxin complex / quorum sensing / rRNA catabolic process / 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 / quorum sensing / rRNA catabolic process / 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 / regulation of DNA-templated transcription / protein-containing complex binding / 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1893
Polymers26,1662
Non-polymers231
Water1629
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-14 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.816, 52.816, 191.398
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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 (strain K12) (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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Disodium Citrate pH 7.5, 20% 2-propanol, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.8→19.63 Å / Num. obs: 8844 / % possible obs: 97.5 % / Redundancy: 6.6 % / Rsym value: 0.132 / Net I/σ(I): 8.3
Reflection shellHighest resolution: 2.8 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 848 / Rsym value: 0.921 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ub4

1ub4


Resolution: 2.8→19.63 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2998 320 4.46 %
Rwork0.2362 --
obs0.2387 7173 96.87 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.869 Å2 / ksol: 0.285 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.177 Å2-0 Å2-0 Å2
2--6.177 Å20 Å2
3----12.3539 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 1 9 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041585
X-RAY DIFFRACTIONf_angle_d0.912164
X-RAY DIFFRACTIONf_dihedral_angle_d15.148560
X-RAY DIFFRACTIONf_chiral_restr0.07251
X-RAY DIFFRACTIONf_plane_restr0.003276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-3.52440.30211620.2627352299
3.52440.29891580.2287333194
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)
18.66712.37774.74645.47553.69938.54370.16020.3399-0.0319-0.06410.2062-0.1666-0.41080.091-0.3070.3379-0.02210.09560.40350.04830.3852-9.829220.65795.6353
24.02891.61673.93355.82736.62175.88971.0599-0.804-0.10141.267-0.3194-0.4020.9634-0.4640.13440.6591-0.2691-0.05650.50150.26260.3688-2.966426.730625.28
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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