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- PDB-6y2q: Escherichia coli RnlA endoribonuclease -

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Basic information

Entry
Database: PDB / ID: 6y2q
TitleEscherichia 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 / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2794
Polymers80,2082
Non-polymers712
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-36 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.320, 100.800, 154.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 40 or (resid 41...
21(chain B and ((resid 3 and (name CA or name...

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
11ILEILESERSER(chain A and (resid 3 through 40 or (resid 41...AA3 - 403 - 40
12ARGARGALAALA(chain A and (resid 3 through 40 or (resid 41...AA41 - 4241 - 42
13ILEILEVALVAL(chain A and (resid 3 through 40 or (resid 41...AA3 - 3573 - 357
14ILEILEVALVAL(chain A and (resid 3 through 40 or (resid 41...AA3 - 3573 - 357
15ILEILEVALVAL(chain A and (resid 3 through 40 or (resid 41...AA3 - 3573 - 357
16ILEILEVALVAL(chain A and (resid 3 through 40 or (resid 41...AA3 - 3573 - 357
21ILEILEILEILE(chain B and ((resid 3 and (name CA or name...BB33
22ILEILEVALVAL(chain B and ((resid 3 and (name CA or name...BB3 - 3573 - 357
23ILEILEVALVAL(chain B and ((resid 3 and (name CA or name...BB3 - 3573 - 357

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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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52129, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein Buffer: 20 mM Tris HCl pH 8, 150 mM NaCl, 1 mM tris(2-carboxyethyl) phosphine. Reservoir solution: 0.1 M MES monohydrate pH 6.5, 12% PEG 20 000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.986→47.9 Å / Num. obs: 20825 / % possible obs: 98.93 % / Redundancy: 7 % / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 9.36
Reflection shellResolution: 2.986→3.092 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.12 / Num. unique obs: 1869 / CC1/2: 0.509 / CC star: 0.822 / % possible all: 90.42

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4i8o

4i8o


Resolution: 2.99→47.9 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1923 4.95 %
Rwork0.1996 36915 -
obs0.2021 20809 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.99 Å2 / Biso mean: 81.74 Å2 / Biso min: 43.38 Å2
Refinement stepCycle: final / Resolution: 2.99→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5367 0 2 3 5372
Biso mean--75.39 54.87 -
Num. residues----692
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1988X-RAY DIFFRACTION2.823TORSIONAL
12B1988X-RAY DIFFRACTION2.823TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.99-3.060.36851230.34042284240785
3.06-3.140.38491360.330826472783100
3.14-3.240.34111360.300426782814100
3.24-3.340.33561360.287426712807100
3.34-3.460.33221420.282926372779100
3.46-3.60.35861390.26326842823100
3.6-3.760.26711380.214126532791100
3.76-3.960.25981430.201926652808100
3.96-4.210.24481360.180626462782100
4.21-4.530.18241400.145626982838100
4.53-4.990.18871410.142326722813100
4.99-5.710.19621410.159826532794100
5.71-7.190.28221330.20626802813100
7.19-47.90.21441390.175426472786100
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)
12.33770.35950.10750.28760.50630.74990.0484-0.2225-0.06220.1622-0.0949-0.0240.3012-0.0510.05850.66430.042-0.040.58340.00540.460124.8862.4271.797
21.85310.208-0.1170.41860.34340.3045-0.07150.1639-0.11550.13270.08990.03170.1975-0.0506-0.02950.63950.006-0.00110.5777-0.09160.63010.031-23.29736.557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:357 )A3 - 357
2X-RAY DIFFRACTION2( CHAIN B AND RESID 3:357 )B3 - 357

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