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- PDB-6y2p: Escherichia coli RnlA-RnlB Toxin-Antitoxin System. -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6y2p
TitleEscherichia coli RnlA-RnlB Toxin-Antitoxin System.
Components
  • Antitoxin RnlB
  • mRNA endoribonuclease toxin LS
KeywordsTOXIN / Prokaryotic Toxin-Antitoxin System / Endoribonuclease / HEPN protein / T4 phage denfense / Antitoxin
Function / homology
Function and homology information


negative regulation of endoribonuclease activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / protein homodimerization activity / cytoplasm
Similarity search - Function
Antitoxin RnlB/LsoB / Antitoxin to bacterial toxin RNase LS or RnlA / Bacterial toxin, RNase RnlA/LsoA, N-terminal / Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain / Bacterial toxin, RNase RnlA/LsoA, DBD domain / RNase LS, bacterial toxin / RNase LS, bacterial toxin DBD domain / RNase LS, bacterial toxin N-terminal
Similarity search - Domain/homology
mRNA endoribonuclease toxin LS / Antitoxin RnlB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsGarcia-Rodriguez, G. / Talavera Perez, A. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0B25.15N Belgium
Citation
Journal: Nucleic Acids Res. / Year: 2021
Title: Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA.
Authors: Garcia-Rodriguez, G. / Charlier, D. / Wilmaerts, D. / Michiels, J. / Loris, R.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2020
Title: The Escherichia coli RnlA-RnlB toxin-antitoxin complex: production, characterization and crystallization.
Authors: Garcia-Rodriguez, G. / Talavera Perez, A. / Konijnenberg, A. / Sobott, F. / Michiels, J. / Loris, R.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA endoribonuclease toxin LS
B: mRNA endoribonuclease toxin LS
C: Antitoxin RnlB
D: Antitoxin RnlB


Theoretical massNumber of molelcules
Total (without water)110,1284
Polymers110,1284
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Isolated RnlA is present as a dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-50 kcal/mol
Surface area40330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.320, 133.580, 55.640
Angle α, β, γ (deg.)90.000, 95.110, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...
21(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC11
12GLYGLYGLYGLY(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1111
13GLUGLUGLUGLU(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC4747
14METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
15METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
16METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
17METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
18METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
21METMETMETMET(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD11
22GLYGLYGLYGLY(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1111
23LYSLYSLYSLYS(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1414
24METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120
25METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120
26METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120
27METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120
28METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120

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Components

#1: Protein mRNA endoribonuclease toxin LS / RNase LS / Toxin LS


Mass: 40104.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rnlA, std, yfjN, b2630, JW2611 / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52129, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin RnlB


Mass: 14960.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rnlB, yfjO, b2631, JW5418 / Plasmid: pET28a
Details (production host): It was expressed as the rnlAB operon cloned into pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52130
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein Buffer: 20 mM Tris HCl pH 8, 150 mM NaCl, 1 mM tris (2-carboxyethyl) phosphine. Reservoir solution: 0.1 M Tris HCl pH 8.5, 25 % (w/v) SOKALAN CP 5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980073 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980073 Å / Relative weight: 1
ReflectionResolution: 2.64→48.78 Å / Num. obs: 51657 / % possible obs: 99.2 % / Redundancy: 6.77 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.1
Reflection shellResolution: 2.64→2.73 Å / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 4871

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8O

4i8o


Resolution: 2.64→48.78 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.68
RfactorNum. reflection% reflection
Rfree0.242 2576 4.99 %
Rwork0.197 49010 -
obs0.199 51586 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 237.75 Å2 / Biso mean: 96.03 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.64→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6975 0 0 27 7002
Biso mean---66.23 -
Num. residues----943
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C688X-RAY DIFFRACTIONPOSITIONAL0
12D688X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.64-2.690.30541180.30182291240985
2.69-2.740.27651450.25327532898100
2.74-2.80.27821440.255227322876100
2.8-2.870.30181430.263927142857100
2.87-2.940.36651470.29227842931100
2.94-3.020.2881420.257927002842100
3.02-3.110.30261450.246827462891100
3.11-3.210.32071440.233327382882100
3.21-3.320.30011440.235727262870100
3.32-3.460.26711450.224527662911100
3.46-3.610.23831440.212827222866100
3.61-3.810.24041440.186927602904100
3.81-4.040.21451450.170927642909100
4.04-4.360.211440.163227302874100
4.36-4.790.19311450.159627542899100
4.79-5.490.2251450.178427572902100
5.49-6.910.28521460.215127772923100
6.91-48.780.20511460.16962796294299
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)
15.8736-3.2352-2.69497.43025.71136.9317-0.59990.823-1.3628-0.59570.34490.26630.9726-0.28110.54041.054-0.21080.1560.5859-0.09551.255372.351-27.309155.1919
26.9699-3.0655-3.51866.41345.87456.7531-0.58860.0112-1.2875-0.41120.7737-1.24140.6730.67880.00971.26080.03060.27170.7307-0.04321.69881.2051-31.750655.0763
32.55851.03310.32876.4865-0.1682.0231-0.1885-0.0232-0.66790.44270.11390.46410.4983-0.09150.18720.9011-0.22280.02490.5641-0.01490.748765.5539-19.151463.0201
44.03640.7091-1.12772.71310.02352.2183-0.2393-1.4527-0.881.8216-0.88740.88981.38030.53420.35992.377-0.25870.58021.06480.21161.219458.9193-25.131881.3105
53.57050.6666-1.74482.95050.47493.3223-0.4469-0.6051-0.50592.24440.27230.6890.72140.33860.52191.5962-0.10630.24090.8330.10161.042262.0948-19.80675.6713
62.30170.7324-1.35191.9426-1.0082.2559-0.48340.5705-0.46660.62180.12111.48450.9202-0.48640.23370.9626-0.26770.25160.7863-0.18311.229156.6376-14.044966.4663
72.522-0.2839-0.97921.9782-0.42071.97860.0910.2511-0.3933-0.2299-0.20610.18210.2873-0.3412-0.02340.4415-0.0869-0.08370.6228-0.06420.366478.305-0.699948.3633
82.5970.0925-1.85534.83922.69852.9302-0.0526-0.0006-0.18750.00360.23660.3048-0.84190.7034-0.30020.7417-0.05130.0121.0337-0.00110.380192.0379.982931.2178
91.5072-1.3609-2.5073.13163.74098.7801-0.26050.66590.1545-0.31260.21730.4361-0.32640.2928-0.07190.49750.0043-0.06810.72570.01950.397483.300210.464937.1332
101.487-0.2528-0.51462.29471.81175.1282-0.09530.31130.0422-0.3132-0.12950.3091-0.1344-0.67660.25050.44380.0124-0.07910.57460.01810.390277.437211.079347.3116
115.8491-6.606-0.21837.40730.15721.8535-0.5962-0.7302-0.70571.18730.52531.8043-1.7992-0.6875-0.07162.00290.170.33580.9544-0.0761.997841.008313.718780.0104
128.5672-0.3494-1.53936.35211.46467.1931-0.2751.65040.4753-1.2042-0.20082.4842-0.3589-1.39840.44571.0028-0.0521-0.46221.0892-0.0411.570547.9725-1.674156.0229
132.2389-0.11890.06422.29150.35452.62780.0161-0.1680.22230.185-0.0288-0.1082-0.2070.1744-0.01010.4233-0.0699-0.05160.5037-0.0240.300188.878212.095263.142
146.5938-1.9065-4.00845.0856.22238.0947-0.4934-0.09050.7375-0.7241.1485-0.3225-2.4413-1.4574-0.49631.48720.2320.0840.79220.21420.820579.58936.947242.3324
158.2642-0.1779-2.01833.1575-3.06513.5496-0.28470.08772.0683-0.8682-0.5273-0.2867-2.3672-0.63080.36881.53830.4927-0.2950.71680.02031.195976.323642.127348.832
165.8764.77230.17848.14995.74187.7011-0.07180.41390.17-1.13120.2619-0.9725-1.10110.28930.06490.74750.09740.06280.63630.13260.59683.944826.997445.1301
173.06464.3529-0.05757.60981.67192.1658-0.24380.8421.6242-1.97520.8222-0.8054-1.8960.5363-0.1551.2696-0.04840.19390.82880.17991.100488.275140.335345.8628
183.87213.70713.2553.69592.46826.1430.33510.36982.00611.0358-0.31790.4257-1.54340.4633-0.18941.42450.0649-0.16350.678-0.01361.251681.380841.955851.6332
198.20963.23582.21272.1127-0.03576.48160.0966-0.41950.9391-0.6122-0.41430.7612-1.0453-0.71790.32570.69750.2383-0.02310.596-0.02330.624575.846128.735652.3511
204.9890.3083-3.63975.38664.82267.53730.1061-0.02362.17320.91540.6576-0.7-2.0587-0.0097-0.46691.53480.0972-0.24170.57420.0481.130584.436137.497258.0375
213.5508-4.5093-1.64635.88162.80934.1236-0.7515-0.6304-0.09741.433-0.15921.0923-1.3988-2.17750.91770.9930.4276-0.03391.0559-0.15281.19866.518334.060455.6141
223.8006-1.7179-1.25928.88225.75957.1950.20090.20670.5215-1.25-0.39580.9758-1.4325-0.75920.36120.84860.358-0.14150.96480.06690.779470.578630.393139.8897
231.7422.586-2.04994.2778-3.82923.83340.60270.11162.2923-0.66170.47643.29260.2146-1.4346-0.90010.8280.0958-0.30591.4963-0.04951.693464.613421.559641.7917
248.1006-5.0338-4.88826.51834.04777.09940.010.4111-0.466-0.51850.3865-0.1145-0.11660.9103-0.43260.4792-0.1014-0.11150.7627-0.09360.5373108.4729-6.448446.1434
256.2318-4.3245-3.6989.13084.87293.13840.03490.7504-0.585-0.31760.1173-0.29940.22870.1115-0.05770.5545-0.0508-0.06030.7031-0.10320.5507101.3925-10.010148.2111
267.0791-0.8308-0.38168.64451.83227.1979-0.05551.1028-0.9855-0.31-0.0486-0.0384-0.039-0.4218-0.17640.4234-0.0678-0.06250.7461-0.27950.618399.0963-13.494844.3782
278.50662.71552.98574.57742.9148.87290.3162-0.2416-0.63440.17690.0627-0.73180.16710.9921-0.47540.4380.0053-0.04310.62710.07530.4142108.5045-7.17960.7269
289.0172-5.841-5.36863.82153.23484.772-1.0425-1.797-1.65421.76580.27930.20851.76731.43081.00231.15490.05010.00221.0240.08510.6042101.4174-6.365768.7387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 26 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 27 THROUGH 77 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 78 THROUGH 113 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 114 THROUGH 143 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 144 THROUGH 169 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 170 THROUGH 203 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 204 THROUGH 267 )A0
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 268 THROUGH 300 )A0
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 301 THROUGH 321 )A0
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 322 THROUGH 357 )A0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 4 THROUGH 99 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 100 THROUGH 189 )B0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 190 THROUGH 357 )B0
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 1 THROUGH 7 )C0
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 8 THROUGH 19 )C0
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 20 THROUGH 28 )C0
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 29 THROUGH 39 )C0
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 40 THROUGH 51 )C0
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 52 THROUGH 68 )C0
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 69 THROUGH 81 )C0
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 82 THROUGH 87 )C0
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 88 THROUGH 111 )C0
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 112 THROUGH 120 )C0
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 1 THROUGH 39 )D0
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 40 THROUGH 68 )D0
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 69 THROUGH 87 )D0
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 88 THROUGH 111 )D0
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 112 THROUGH 120 )D0

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