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- PDB-5ckd: E. coli MazF E24A form III -

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Basic information

Entry
Database: PDB / ID: 5ckd
TitleE. coli MazF E24A form III
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: 1.698 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
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-20 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.858, 32.462, 85.263
Angle α, β, γ (deg.)90.00, 98.79, 90.00
Int Tables number5
Space group name H-MC121

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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)
Strain: K12 / 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.: 87 / 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: 1.83 Å3/Da / Density % sol: 32.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 0.2M Litium Sulfate, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.7→30.36 Å / Num. obs: 20637 / % possible obs: 97.9 % / Redundancy: 3.3 % / Rsym value: 0.043 / Net I/av σ(I): 16.7 / Net I/σ(I): 16.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.8 / % possible all: 97.2

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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: 1.698→30.357 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 1060 5.14 %
Rwork0.1972 --
obs0.1997 20627 97.2 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.042 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9699 Å2-0 Å20.3255 Å2
2--12.2518 Å20 Å2
3----10.2819 Å2
Refinement stepCycle: LAST / Resolution: 1.698→30.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 1 87 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091684
X-RAY DIFFRACTIONf_angle_d1.2412292
X-RAY DIFFRACTIONf_dihedral_angle_d11.126612
X-RAY DIFFRACTIONf_chiral_restr0.081262
X-RAY DIFFRACTIONf_plane_restr0.006295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6982-1.77550.31711200.29152391X-RAY DIFFRACTION96
1.7755-1.86910.2451380.22722412X-RAY DIFFRACTION97
1.8691-1.98620.25891350.20042428X-RAY DIFFRACTION98
1.9862-2.13950.2651240.18892481X-RAY DIFFRACTION97
2.1395-2.35470.25251240.18722427X-RAY DIFFRACTION98
2.3547-2.69530.24031250.20872471X-RAY DIFFRACTION97
2.6953-3.3950.23951390.18772449X-RAY DIFFRACTION97
3.395-30.36230.23251550.1932508X-RAY DIFFRACTION97
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)
11.8511-1.395-0.78711.65491.09472.3690.10550.2408-0.339-0.048-0.17670.33570.2738-0.3268-0.23220.08240.0121-0.04470.0475-0.00990.056-7.97692.535910.8724
23.6339-0.9119-0.73441.01431.24363.8039-0.0336-0.4525-0.34140.12160.07640.0080.26470.1678-0.01380.1049-0.0217-0.01030.22610.01640.1772-1.76915.559929.9529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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