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- PDB-5co7: E. coli MazF form III -

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Basic information

Entry
Database: PDB / ID: 5co7
TitleE. coli MazF 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: 3.489 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 19, 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
C: Endoribonuclease MazF
D: Endoribonuclease MazF
E: Endoribonuclease MazF
F: Endoribonuclease MazF


Theoretical massNumber of molelcules
Total (without water)77,6456
Polymers77,6456
Non-polymers00
Water00
1
A: Endoribonuclease MazF
B: Endoribonuclease MazF


Theoretical massNumber of molelcules
Total (without water)25,8822
Polymers25,8822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-12 kcal/mol
Surface area10400 Å2
MethodPISA
2
C: Endoribonuclease MazF
D: Endoribonuclease MazF


Theoretical massNumber of molelcules
Total (without water)25,8822
Polymers25,8822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-14 kcal/mol
Surface area10140 Å2
MethodPISA
3
E: Endoribonuclease MazF
F: Endoribonuclease MazF


Theoretical massNumber of molelcules
Total (without water)25,8822
Polymers25,8822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-14 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.050, 129.050, 299.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 12940.904 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mazF, chpA, chpAK, b2782, JW2753 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AE70, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Imidazole pH 6.5, 1M Sodium Acetate

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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: 3.49→50.02 Å / Num. obs: 32860 / % possible obs: 99.4 % / Redundancy: 14.6 % / Rsym value: 0.15 / Net I/σ(I): 12.85
Reflection shellResolution: 3.49→3.7 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.8 / % possible all: 96.5

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Processing

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

1ub4


Resolution: 3.489→50.02 Å / SU ML: 0.97 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3214 1641 5 %
Rwork0.276 --
obs0.2783 32839 99.37 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 139.151 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8996 Å20 Å2-0 Å2
2--5.8996 Å20 Å2
3----11.7993 Å2
Refinement stepCycle: LAST / Resolution: 3.489→50.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4445 0 0 0 4445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094579
X-RAY DIFFRACTIONf_angle_d1.4546247
X-RAY DIFFRACTIONf_dihedral_angle_d16.6251564
X-RAY DIFFRACTIONf_chiral_restr0.091731
X-RAY DIFFRACTIONf_plane_restr0.007799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.489-3.59170.3271250.29532392X-RAY DIFFRACTION93
3.5917-3.70760.34441350.27542558X-RAY DIFFRACTION100
3.7076-3.840.32841340.26242543X-RAY DIFFRACTION100
3.84-3.99370.32131350.25022567X-RAY DIFFRACTION100
3.9937-4.17540.29241370.25492597X-RAY DIFFRACTION100
4.1754-4.39540.28211350.23452563X-RAY DIFFRACTION100
4.3954-4.67060.25331370.22442610X-RAY DIFFRACTION100
4.6706-5.03090.28661360.24382587X-RAY DIFFRACTION100
5.0309-5.53660.31711380.27572625X-RAY DIFFRACTION100
5.5366-6.33640.32161380.2942636X-RAY DIFFRACTION100
6.3364-7.9780.39711420.30642688X-RAY DIFFRACTION100
7.978-50.02550.34531490.31422832X-RAY DIFFRACTION99
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)
15.8346-0.32254.0025.9763-0.06735.91630.04220.00940.2143-0.0081-0.3583-0.1734-0.6257-0.05890.38240.4757-0.025-0.15620.59920.07750.41549.2851-30.014324.1338
24.2545-0.79630.21746.2813-2.3037.02180.14740.438-0.15390.1686-0.15-0.0812-0.35220.5050.02480.63260.0138-0.12180.89990.12090.435622.2211-42.968532.7268
35.636-0.012-1.41966.0038-1.66583.5626-0.1459-0.0158-0.10470.4172-0.3317-0.5089-0.52570.01070.45820.90850.1039-0.05740.39680.15540.690833.9413-72.890962.3007
43.1262-1.01460.64535.1408-2.99725.31370.30560.58460.40270.5069-0.24280.0785-0.59350.06060.05491.21320.0383-0.04180.50230.2310.525726.4233-55.547655.2669
53.9077-1.4677-1.90575.71722.38466.258-0.0671-0.072-0.14410.2619-0.1513-0.14120.5495-0.03260.22360.99050.0057-0.08150.4019-0.0430.66432.427-12.24983.0584
61.4789-0.1203-0.48424.26250.32581.32220.05490.1293-0.3751-0.6653-0.03450.41210.1796-0.13890.18550.7874-0.0345-0.2585-0.02420.02980.864225.4719-31.158681.2118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain 'A'
2X-RAY DIFFRACTION2Chain 'B'
3X-RAY DIFFRACTION3Chain 'C'
4X-RAY DIFFRACTION4Chain 'D'
5X-RAY DIFFRACTION5Chain 'E'
6X-RAY DIFFRACTION6Chain 'F'

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