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- PDB-7aex: NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA... -

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Basic information

Entry
Database: PDB / ID: 7aex
TitleNRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuclease
ComponentsmRNA endoribonuclease toxin LS
KeywordsTOXIN / Endoribonuclease / HEPN protein / T4 phage denfense / Toxin-Antitoxin System
Function / homology
Function and homology information


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
Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain / Bacterial toxin, RNase RnlA/LsoA, DBD domain / Bacterial toxin, RNase RnlA/LsoA, N-terminal / RNase LS, bacterial toxin / RNase LS, bacterial toxin DBD domain / RNase LS, bacterial toxin N-terminal
Similarity search - Domain/homology
mRNA endoribonuclease toxin LS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGarcia-Rodriguez, G. / 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
DepositionSep 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 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 31, 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

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Assembly

Deposited unit
A: mRNA endoribonuclease toxin LS


Theoretical massNumber of molelcules
Total (without water)31,1491
Polymers31,1491
Non-polymers00
Water2,954164
1
A: mRNA endoribonuclease toxin LS

A: mRNA endoribonuclease toxin LS


Theoretical massNumber of molelcules
Total (without water)62,2982
Polymers62,2982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1790 Å2
ΔGint-16 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.658, 81.676, 54.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 31148.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rnlA, std, yfjN, b2630, JW2611
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52129, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.66 Å3/Da / Density % sol: 53.8 % / Description: plates
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M NaCl; 0.1 M BIS-Tris; pH 5.5; 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.946→45.19 Å / Num. obs: 23246 / % possible obs: 96.47 % / Redundancy: 13.1 % / Biso Wilson estimate: 29.65 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 12.72
Reflection shellResolution: 1.946→2.015 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 1700 / CC1/2: 0.469 / CC star: 0.799 / % possible all: 74.17

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS1.17.1_3660data processing
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4i80

4i80


Resolution: 1.95→45.19 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.7896
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1871 8.82 %
Rwork0.1861 19331 -
obs0.1904 21202 90.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.77 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 0 164 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712154
X-RAY DIFFRACTIONf_angle_d0.86362928
X-RAY DIFFRACTIONf_chiral_restr0.0539342
X-RAY DIFFRACTIONf_plane_restr0.0052372
X-RAY DIFFRACTIONf_dihedral_angle_d15.9623289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.3585840.332903X-RAY DIFFRACTION56.56
2-2.060.3731070.29051167X-RAY DIFFRACTION72.47
2.06-2.120.29551290.26361326X-RAY DIFFRACTION82.62
2.12-2.20.251380.23421427X-RAY DIFFRACTION89.12
2.2-2.290.31561490.2151508X-RAY DIFFRACTION93.04
2.29-2.390.28741520.20261549X-RAY DIFFRACTION94.82
2.39-2.520.25841470.19591560X-RAY DIFFRACTION96.5
2.52-2.680.23451530.18341595X-RAY DIFFRACTION97.44
2.68-2.880.25061580.21291597X-RAY DIFFRACTION98.21
2.88-3.170.26961580.21361618X-RAY DIFFRACTION98.39
3.17-3.630.23731610.18281646X-RAY DIFFRACTION99.67
3.63-4.570.1871630.14251666X-RAY DIFFRACTION99.95
4.58-45.190.19271720.1571769X-RAY DIFFRACTION99.85
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)
17.17155457926-2.993637906220.6796797267976.107935461190.9200749407143.9588211407-0.02845583022660.06004475081340.03749296933540.166965219881-0.05354043812990.0971362948080.2126109475510.122119926260.04221080442350.269443096347-0.04681551734150.06701667589940.206614952130.06871815875160.1729615459296.5686595646524.349355484218.7323929911
24.41759432846-2.866839111340.1490508528478.25078345399-2.765288002845.222879316870.08837684200980.1827930747480.428620612437-0.0282733552532-0.39744471799-0.563378816355-0.1234960557190.5570022149730.1148846561710.212907347142-0.03967399865010.02491333668680.184211730504-0.002271269533270.2275949779275.9194978183134.990395102316.3911573598
35.77314756152-2.21183098976-0.1246911695539.183217553420.5017848781964.383769749250.227986766090.266195129145-0.520580064050.0821221388692-0.338320587234-0.778920369744-0.1087208629920.4244148374280.1432735341410.284126410983-0.00807069785328-0.003358095006770.2432745280120.07185951420620.2994636681727.4282774862429.496687143114.518090213
44.31050591878-2.26504935364-0.3931873336155.10941856884-0.9530836099282.894156945660.0375775679453-0.0184198403343-0.116178365323-0.072149982619-0.172075518255-0.0398559276978-0.01630980765010.3396674374340.2335148864180.194677691805-0.00788610332842-0.00207606772090.198626162969-0.01763168994320.1394028846547.1673872428623.497792796219.7966668789
56.594262277391.63972030494-2.40788153746.98889395722-2.499405925014.46053880361-0.2038260528770.633052731891-0.121284886211-0.5242313889240.2396052733710.0986794302774-0.116758903061-0.2993097906130.02802961259130.322375292867-0.0200768363336-0.05676235238920.211905528062-0.01348413567380.1806592189931.1052290365210.480961372218.020075444
60.8796823642610.3982443721471.361013873955.319594793214.826575465279.12680672299-0.216693990086-0.435897545122-0.0455838726080.270107809401-0.2734654971880.01842272009840.189478695993-0.979501464710.2367491222660.307682888685-0.03639659096950.1263920789370.231221284505-0.01945363276630.390526167571-5.527509619935.6802406151937.257081118
78.09343698088-0.802551481031-3.728635807693.711932281931.872961952036.57779314312-0.07512506021250.240357102295-0.164465414334-0.108173980993-0.026354006658-0.1203183651810.0195518195817-0.2021487529550.08329322097250.198877159457-0.00606857246743-0.03536919726030.177066606680.03673112942730.182971547072.098256866969.9023894184927.3487350728
82.371840484150.360096094854-1.085489520553.797267725514.563323261358.10580253430.144056371957-0.3128633273850.353398539209-0.105150084077-0.0699478875493-0.0972056808738-0.8617997938740.320804568593-0.03791843597940.417559910575-0.0194422497723-0.006298750630750.2678646585380.009942571762930.2409515096327.2768311024524.916324725643.3585372638
96.52870230105-0.454797524881-3.033447546582.264559139380.9781010259313.262128588740.186269589343-0.371938249599-0.08287597389560.381418515242-0.119359668742-0.192924730278-0.3500525958950.360377488407-0.03183147822170.241235125433-0.0411971352041-0.02790073592440.2210442024110.01721770070430.2132404626110.833481769320.168991910942.0551966244
106.639026521632.57091296417-0.8942337479996.34046490804-1.637223471354.727853550.1079561153960.0857136895337-0.2424215951520.335801720267-0.270983329181-0.391366089297-0.544445361080.1255092047370.06817188951650.3093140231082.81119246748E-5-0.02336261149480.357578864676-0.04161491276230.32154832810321.394131727914.415095229427.0523579534
118.34756959081-5.59987379592-6.977810210475.701899163525.416825992365.8019612813-0.375355778766-0.4650355265690.003188108192131.091862397790.217388608818-0.004473722999121.086094073340.1490108309110.2367382602650.346091097513-0.0557177831344-0.0515376360730.3270035262750.02144237725640.2720680795615.782206915979.9722006348139.5234378043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 91 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 203 )
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 221 )
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 246 )
8X-RAY DIFFRACTION8chain 'A' and (resid 247 through 300 )
9X-RAY DIFFRACTION9chain 'A' and (resid 301 through 322 )
10X-RAY DIFFRACTION10chain 'A' and (resid 323 through 336 )
11X-RAY DIFFRACTION11chain 'A' and (resid 337 through 357 )

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