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- PDB-6y2s: Escherichia coli R318A RnlA endoribonuclease (single alanine muta... -

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Basic information

Entry
Database: PDB / ID: 6y2s
TitleEscherichia coli R318A RnlA endoribonuclease (single alanine mutant of RnlA)
ComponentsmRNA endoribonuclease toxin LS
KeywordsTOXIN / Endoribonuclease catalytic mutant / HEPN protein / T4 phage defense / 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: 3.79 Å
AuthorsGarcia-Rodriguez, G. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0B25.15N Belgium
CitationJournal: To Be Published
Title: Quaternary structure changes control ribonuclease activity of RnlA toxin.
Authors: Garcia-Rodriguez, G. / Talavera Perez, A. / Wilmaerts, D. / Michiels, J. / Charlier, D. / Loris, R.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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 area1730 Å2
ΔGint-16 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.560, 105.560, 156.500
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
11ARGARGTYRTYR(chain 'A' and ((resid 4 and (name N or name...AA4 - 14620 - 162
12ASPASPHISHIS(chain 'A' and ((resid 4 and (name N or name...AA148 - 323164 - 339
13SERSERTHRTHR(chain 'A' and ((resid 4 and (name N or name...AA335 - 345351 - 361
14ALAALATYRTYR(chain 'A' and ((resid 4 and (name N or name...AA347 - 355363 - 371
25ARGARGTYRTYR(chain 'B' and (resid 4 through 64 or (resid 65...BB4 - 14620 - 162
26ASPASPHISHIS(chain 'B' and (resid 4 through 64 or (resid 65...BB148 - 323164 - 339
27SERSERTHRTHR(chain 'B' and (resid 4 through 64 or (resid 65...BB335 - 345351 - 361
28ALAALATYRTYR(chain 'B' and (resid 4 through 64 or (resid 65...BB347 - 355363 - 371

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Components

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


Mass: 41899.844 Da / Num. of mol.: 2 / Mutation: R318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
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: 3.18 Å3/Da / Density % sol: 61.34 %
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: 0.4 M Potassium sodium tartrate tetrahydrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980126 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980126 Å / Relative weight: 1
ReflectionResolution: 3.79→46.77 Å / Num. obs: 10617 / % possible obs: 94.39 % / Redundancy: 3.87 % / Biso Wilson estimate: 104.89 Å2 / CC1/2: 0.956 / CC star: 0.989 / Net I/σ(I): 3.61
Reflection shellResolution: 3.79→3.92 Å / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 941 / CC1/2: 0.66

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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: 3.79→46.77 Å / SU ML: 0.7197 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 39.9238
RfactorNum. reflection% reflection
Rfree0.3418 941 5.05 %
Rwork0.2637 --
obs0.2677 10617 90.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 116.58 Å2
Refinement stepCycle: LAST / Resolution: 3.79→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 0 0 5313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00395422
X-RAY DIFFRACTIONf_angle_d0.69757371
X-RAY DIFFRACTIONf_chiral_restr0.0447860
X-RAY DIFFRACTIONf_plane_restr0.0043945
X-RAY DIFFRACTIONf_dihedral_angle_d14.48791957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.79-3.990.37031270.38762292X-RAY DIFFRACTION81.64
3.99-4.240.38161310.35872536X-RAY DIFFRACTION91.21
4.24-4.560.40781370.30322519X-RAY DIFFRACTION91.24
4.56-5.020.42721300.2862580X-RAY DIFFRACTION92.49
5.02-5.750.36141400.27192571X-RAY DIFFRACTION92.56
5.75-7.240.32661370.28872530X-RAY DIFFRACTION90.71
7.24-46.770.25161390.16742673X-RAY DIFFRACTION95.71
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)
18.544047343250.272613731049-0.0493071616460.3507086621040.5393621911130.349260593531-0.477250609403-0.502532161376-0.790311482732-0.148929698560.08698584946820.197258989423-0.247089635588-0.0008785415646740.4113721529840.5974299907450.00474186268769-0.07642362459740.9856558479660.04531249434530.78258541349138.184564816615.5433867769.812321085
22.390076215890.0163837527460.638737400057.07397726640.4648421454013.91658011607-0.2145548049350.283459976702-0.0122099003494-0.2068969586880.03160184590030.292464927410.2585501920190.7429956929740.09068588676060.524860453244-0.04966811345550.1163171008270.865267180446-0.08207833082150.66450128702913.55687851621.3401230748865.3911134536
36.345475989760.03072749336980.6520426053465.58240758996-0.8278352083876.31074494235-0.279235478227-0.928249292189-0.8910922459251.594055175430.400211886988-0.7781385393950.8529396690560.0718806256298-0.1372187318781.42655747460.2626995959740.1095728576471.013061850710.001024244367530.90451061603117.8042460173-9.9883801071880.7845104173
45.63721458797-1.14319996939-0.3639966788550.590998470434-0.3002114844970.04626561615960.04882896499760.236331086130.9303987791490.04209532479990.239984999923-0.02383042121110.3190769668420.240318757122-0.2511913148310.678057381175-0.154438565523-0.04859427741051.25393859977-0.147008332211.34099178425-17.5767892259-15.201252123226.4775270686
55.86815108855-1.269142997911.24255316582.55382593781-0.2459178584696.95477636197-0.4934313822490.1163973544770.148762082617-0.345369886734-0.02219329247170.1066208261130.00627153874413-0.85677358830.4167230048420.5029579887920.0880137387640.05343445721210.813524344383-0.1484844379211.103063946688.9500445472-17.828577743929.0783323433
66.948565432992.65415613398-0.2345798498879.14931577303-1.330716080452.589109257070.00718532987039-0.341428630941-0.98743398502-0.4593634220220.0480506205895-0.08049116118420.6667478812010.53335366312-0.05282841475160.7752777796140.18863009617-0.0677083122560.885607671354-0.3214458352370.85625936154212.32450701-29.729026773347.1980691985
75.554089677114.00908701177-1.40246497563.28681110749-1.592596777535.27576503651-1.33605990363E-50.599291382888-0.2887412126931.7917942171-0.2753104298850.3794537042662.254730992460.305891202402-0.09495541081851.637285511210.2082384844060.006746898639460.9411183270110.1578787983760.541339805625.82188476341-30.825020893149.7779745346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 143 )
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 246 )
3X-RAY DIFFRACTION3chain 'A' and (resid 247 through 356 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 120 )
5X-RAY DIFFRACTION5chain 'B' and (resid 121 through 203 )
6X-RAY DIFFRACTION6chain 'B' and (resid 204 through 300 )
7X-RAY DIFFRACTION7chain 'B' and (resid 301 through 356 )

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