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- PDB-6y2r: Escherichia coli R255A RnlA endoribonuclease (single alanine muta... -

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Basic information

Entry
Database: PDB / ID: 6y2r
TitleEscherichia coli R255A RnlA endoribonuclease (single alanine mutant of RnlA)
ComponentsmRNA endoribonuclease toxin LS
KeywordsTOXIN / Endoribonuclease catalytic mutant / 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: 3.89 Å
AuthorsGarcia-Rodriguez, G. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0B25.15N Belgium
CitationJournal: 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.
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


Theoretical massNumber of molelcules
Total (without water)83,8002
Polymers83,8002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-17 kcal/mol
Surface area33390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.230, 104.930, 152.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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-ID
11
21

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
11ILEILELYSLYS(chain 'A' and ((resid 3 and (name N or name...AA3 - 2719 - 43
12TYRTYRTHRTHR(chain 'A' and ((resid 3 and (name N or name...AA29 - 11045 - 126
13VALVALMETMET(chain 'A' and ((resid 3 and (name N or name...AA112 - 324128 - 340
14ASPASPILEILE(chain 'A' and ((resid 3 and (name N or name...AA336 - 356352 - 372
25ILEILELYSLYS(chain 'B' and (resid 3 through 27 or resid 29...BB3 - 2719 - 43
26TYRTYRTHRTHR(chain 'B' and (resid 3 through 27 or resid 29...BB29 - 11045 - 126
27VALVALMETMET(chain 'B' and (resid 3 through 27 or resid 29...BB112 - 324128 - 340
28ASPASPILEILE(chain 'B' and (resid 3 through 27 or resid 29...BB336 - 356352 - 372

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Components

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


Mass: 41899.844 Da / Num. of mol.: 2 / Mutation: R255A
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

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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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein Buffer: 20 mM Tris HCl pH 8, 150 mM NaCl, 1 mM tris(2-carboxyethyl) phosphine. Reservoir solution: 100 mM Tris-HCl, pH 8.5, 8 % PEG 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980114 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980114 Å / Relative weight: 1
ReflectionResolution: 3.89→45.85 Å / Num. obs: 9959 / % possible obs: 99.61 % / Redundancy: 10.1 % / Biso Wilson estimate: 124.23 Å2 / CC1/2: 0.987 / CC star: 0.997 / Net I/σ(I): 4.44
Reflection shellResolution: 3.89→4.03 Å / Rmerge(I) obs: 2.311 / Num. unique obs: 977 / CC1/2: 0.549 / % possible all: 98.29

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Processing

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

4i8o


Resolution: 3.89→45.85 Å / SU ML: 0.6858 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.9072
RfactorNum. reflection% reflection
Rfree0.3009 904 4.96 %
Rwork0.2107 --
obs0.215 9946 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 137.15 Å2
Refinement stepCycle: LAST / Resolution: 3.89→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 0 0 5386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00375505
X-RAY DIFFRACTIONf_angle_d0.69277478
X-RAY DIFFRACTIONf_chiral_restr0.0463866
X-RAY DIFFRACTIONf_plane_restr0.0042961
X-RAY DIFFRACTIONf_dihedral_angle_d15.64622014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.89-4.140.36871550.32622860X-RAY DIFFRACTION98.37
4.14-4.460.37681500.272914X-RAY DIFFRACTION99.84
4.46-4.90.30591550.2362903X-RAY DIFFRACTION99.9
4.9-5.610.31421490.22172862X-RAY DIFFRACTION99.77
5.62-7.070.34381470.23692904X-RAY DIFFRACTION99.9
7.07-49.180.22771480.1392895X-RAY DIFFRACTION99.9
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)
14.83040554525-0.4001658065410.7182179782050.2424610005710.1919372147360.31641508306-0.1189740713470.5968682483260.5703407460520.1460003659350.03704426128260.109728719944-0.0208780219558-0.50843124792-0.02516721799740.9947668036110.168546933920.01847084790751.02749757779-0.04894806892321.1429332734446.4675290428-66.9492144829-66.1618192062
22.85145244916-1.805784490460.9037520075016.870883403914.372450810735.406824063840.1916455923940.418219842045-0.5906288327650.167641917440.438027697337-0.2182890694780.2869442884451.3227263868-0.4992104264620.7959465795640.00777419179535-0.07815022674070.83481481634-0.0005774195543221.060420109316.1361090624-64.0188276393-69.3936343991
31.743076454530.972402563457-0.5544722156264.3239740668-3.275402947618.89628580532-0.09547328124370.6997757370450.116935309796-0.523238785092-0.176607754186-0.110768789399-0.4683670787530.4571235923540.2046879642311.216816159730.0011220661964-0.07218309591371.21900234771-0.07163267361691.2594031844815.7347602076-42.3865386281-75.5385425909
48.05794747481.524308015780.8196768832093.124863521553.847807741855.22189756245-0.29544463651-0.768145686903-0.12600755089-0.03002461162040.482480111709-0.5530650951270.05586693856490.133968138407-0.1846286866751.203276509280.0656764326349-0.0259571700141.15721603324-0.07840874743481.38380663832-25.4650085407-36.6739336667-25.4374695529
52.44533527401-1.631359166690.5524887720881.043877540450.553674383576.19023841061-0.1702655856840.238951944902-0.002182228104330.09635178033460.08080614594850.2142952188560.3993266825420.382904872060.03804828213980.952066521332-0.07849675656760.05980334816071.00023561728-0.05745738535671.1496933999510.7401210516-33.0270025821-35.0788347414
63.90792660389-0.6548915734431.426179889093.816617763620.2986571673165.12626794083-0.312373762083-0.06486801079541.46861331192-0.2053202038310.8554434674870.274334950509-1.419631037890.94257977786-0.3850560692491.941496248140.04116992172420.08446986193321.27915834659-0.05428715231071.547164214818.56584190759-16.1674305505-46.2603253728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 203 )
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 356 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 91 )
5X-RAY DIFFRACTION5chain 'B' and (resid 92 through 246 )
6X-RAY DIFFRACTION6chain 'B' and (resid 247 through 356 )

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