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- PDB-5ck9: E. coli MazF form I -

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Basic information

Entry
Database: PDB / ID: 5ck9
TitleE. coli MazF 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 / regulation of growth / positive regulation of programmed cell death / 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 / regulation of growth / positive regulation of programmed cell death / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsZorzini, V. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek Vlaanderen (FWO) Belgium
Biostruct-X
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)26,5975
Polymers25,8822
Non-polymers7153
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-18 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.190, 52.190, 197.840
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: 12940.904 Da / Num. of mol.: 2
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: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Disodium Citrate pH 5.6, 0.2M Ammonium Acetate, 30%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: Feb 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.898→41.11 Å / Num. obs: 23960 / % possible obs: 99.4 % / Redundancy: 11.2 % / Rsym value: 0.092 / Net I/σ(I): 17.68
Reflection shellResolution: 1.898→2.01 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.64 / Rsym value: 1.328 / % possible all: 97

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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: 1.898→41.11 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 1194 5 %
Rwork0.1938 --
obs0.1959 23878 99.45 %
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 90.766 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.6496 Å2-0 Å2-0 Å2
2--7.6496 Å20 Å2
3----15.2993 Å2
Refinement stepCycle: LAST / Resolution: 1.898→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 48 112 1723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071677
X-RAY DIFFRACTIONf_angle_d1.0522267
X-RAY DIFFRACTIONf_dihedral_angle_d12.622626
X-RAY DIFFRACTIONf_chiral_restr0.072257
X-RAY DIFFRACTIONf_plane_restr0.004283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.97370.39391300.34232459X-RAY DIFFRACTION97
1.9737-2.06350.27161320.25962523X-RAY DIFFRACTION100
2.0635-2.17230.28321340.2242531X-RAY DIFFRACTION100
2.1723-2.30840.2361320.1932495X-RAY DIFFRACTION99
2.3084-2.48660.22751340.16992543X-RAY DIFFRACTION100
2.4866-2.73670.23521330.18192530X-RAY DIFFRACTION100
2.7367-3.13260.19461330.15932517X-RAY DIFFRACTION100
3.1326-3.94630.22231330.16982541X-RAY DIFFRACTION100
3.9463-41.11950.23861330.2042545X-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)
15.12281.16011.34172.63921.60245.93320.09130.37610.2407-0.04890.00030.0824-0.01160.0958-0.10460.11660.0009-0.00430.23820.00140.1661-9.146621.27534.894
22.14061.89781.05584.4381.00034.36830.2658-0.18670.20690.7075-0.06150.11830.20.4414-0.11420.2729-0.0760.01860.0896-0.00750.1253-3.113927.030524.209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain 'A'
2X-RAY DIFFRACTION2Chain 'B'

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