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- PDB-7d8o: Crystal structure of E. coli ToxIN type III toxin-antitoxin complex -

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Basic information

Entry
Database: PDB / ID: 7d8o
TitleCrystal structure of E. coli ToxIN type III toxin-antitoxin complex
Components
  • Antitoxin RNA
  • Type III toxin-antitoxin system ToxN/AbiQ family toxin
KeywordsTOXIN/RNA / Toxin-antitoxin complex / ToxIN / endoribonuclease / RNA pseudoknot / RNA-protein complex / TOXIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsManikandan, P. / Rothweiler, U. / Singh, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Identification, functional characterization, assembly and structure of ToxIN type III toxin-antitoxin complex from E. coli.
Authors: Manikandan, P. / Sandhya, S. / Nadig, K. / Paul, S. / Srinivasan, N. / Rothweiler, U. / Singh, M.
History
DepositionOct 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Type III toxin-antitoxin system ToxN/AbiQ family toxin
B: Antitoxin RNA
C: Type III toxin-antitoxin system ToxN/AbiQ family toxin
D: Antitoxin RNA
E: Type III toxin-antitoxin system ToxN/AbiQ family toxin
F: Antitoxin RNA
G: Type III toxin-antitoxin system ToxN/AbiQ family toxin
H: Antitoxin RNA
I: Type III toxin-antitoxin system ToxN/AbiQ family toxin
J: Antitoxin RNA
K: Type III toxin-antitoxin system ToxN/AbiQ family toxin
L: Antitoxin RNA


Theoretical massNumber of molelcules
Total (without water)201,69612
Polymers201,69612
Non-polymers00
Water8,971498
1
A: Type III toxin-antitoxin system ToxN/AbiQ family toxin
B: Antitoxin RNA
C: Type III toxin-antitoxin system ToxN/AbiQ family toxin
D: Antitoxin RNA
E: Type III toxin-antitoxin system ToxN/AbiQ family toxin
F: Antitoxin RNA


Theoretical massNumber of molelcules
Total (without water)100,8486
Polymers100,8486
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-70 kcal/mol
Surface area34270 Å2
MethodPISA
2
G: Type III toxin-antitoxin system ToxN/AbiQ family toxin
H: Antitoxin RNA
I: Type III toxin-antitoxin system ToxN/AbiQ family toxin
J: Antitoxin RNA
K: Type III toxin-antitoxin system ToxN/AbiQ family toxin
L: Antitoxin RNA


Theoretical massNumber of molelcules
Total (without water)100,8486
Polymers100,8486
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14050 Å2
ΔGint-74 kcal/mol
Surface area33990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.630, 86.643, 123.568
Angle α, β, γ (deg.)90.000, 91.660, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 11 or resid 13...
21(chain C and (resid 0 through 11 or resid 13...
31(chain E and ((resid 0 through 1 and (name N...
41(chain G and ((resid 0 through 1 and (name N...
51(chain I and (resid 0 through 11 or resid 13...
61(chain K and ((resid 0 through 1 and (name N...
12(chain B and (resid -3 through 17 or resid 22 through 33))
22(chain D and (resid -3 through 17 or resid 22 through 33))
32(chain F and (resid -3 through 17 or resid 22 through 33))
42(chain H and (resid -3 through 17 or resid 22 through 33))
52(chain J and (resid -3 through 17 or resid 22 through 33))
62(chain L and (resid -3 through 17 or resid 22 through 33))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETILEILE(chain A and (resid 0 through 11 or resid 13...AA0 - 1112 - 23
121TYRTYRILEILE(chain A and (resid 0 through 11 or resid 13...AA13 - 9325 - 105
131ALAALALEULEU(chain A and (resid 0 through 11 or resid 13...AA95 - 102107 - 114
141SERSERLYSLYS(chain A and (resid 0 through 11 or resid 13...AA104 - 111116 - 123
151METMETGLYGLY(chain A and (resid 0 through 11 or resid 13...AA113 - 142125 - 154
161METMETLYSLYS(chain A and (resid 0 through 11 or resid 13...AA144 - 162156 - 174
211METMETILEILE(chain C and (resid 0 through 11 or resid 13...CC0 - 1112 - 23
221TYRTYRILEILE(chain C and (resid 0 through 11 or resid 13...CC13 - 9325 - 105
231ALAALATYRTYR(chain C and (resid 0 through 11 or resid 13...CC95 - 10107 - 22
241METMETLYSLYS(chain C and (resid 0 through 11 or resid 13...CC0 - 16212 - 174
251METMETLYSLYS(chain C and (resid 0 through 11 or resid 13...CC0 - 16212 - 174
261METMETGLYGLY(chain C and (resid 0 through 11 or resid 13...CC144 - 161156 - 173
271METMETLYSLYS(chain C and (resid 0 through 11 or resid 13...CC0 - 16212 - 174
281METMETLYSLYS(chain C and (resid 0 through 11 or resid 13...CC0 - 16212 - 174
291METMETLYSLYS(chain C and (resid 0 through 11 or resid 13...CC0 - 16212 - 174
2101METMETLYSLYS(chain C and (resid 0 through 11 or resid 13...CC0 - 16212 - 174
311METMETALAALA(chain E and ((resid 0 through 1 and (name N...EE0 - 112 - 13
321METMETLYSLYS(chain E and ((resid 0 through 1 and (name N...EE0 - 16212 - 174
331METMETLYSLYS(chain E and ((resid 0 through 1 and (name N...EE0 - 16212 - 174
341METMETLYSLYS(chain E and ((resid 0 through 1 and (name N...EE0 - 16212 - 174
351METMETLYSLYS(chain E and ((resid 0 through 1 and (name N...EE0 - 16212 - 174
411METMETALAALA(chain G and ((resid 0 through 1 and (name N...GG0 - 112 - 13
421METMETLYSLYS(chain G and ((resid 0 through 1 and (name N...GG0 - 16212 - 174
431METMETLYSLYS(chain G and ((resid 0 through 1 and (name N...GG0 - 16212 - 174
441METMETLYSLYS(chain G and ((resid 0 through 1 and (name N...GG0 - 16212 - 174
451METMETLYSLYS(chain G and ((resid 0 through 1 and (name N...GG0 - 16212 - 174
511METMETILEILE(chain I and (resid 0 through 11 or resid 13...II0 - 1112 - 23
521TYRTYRILEILE(chain I and (resid 0 through 11 or resid 13...II13 - 9325 - 105
531ALAALALEULEU(chain I and (resid 0 through 11 or resid 13...II95 - 102107 - 114
541SERSERLYSLYS(chain I and (resid 0 through 11 or resid 13...II104 - 111116 - 123
551METMETGLYGLY(chain I and (resid 0 through 11 or resid 13...II113 - 142125 - 154
561METMETLYSLYS(chain I and (resid 0 through 11 or resid 13...II144 - 162156 - 174
611METMETALAALA(chain K and ((resid 0 through 1 and (name N...KK0 - 112 - 13
621METMETLYSLYS(chain K and ((resid 0 through 1 and (name N...KK0 - 16212 - 174
631METMETLYSLYS(chain K and ((resid 0 through 1 and (name N...KK0 - 16212 - 174
641METMETLYSLYS(chain K and ((resid 0 through 1 and (name N...KK0 - 16212 - 174
651METMETLYSLYS(chain K and ((resid 0 through 1 and (name N...KK0 - 16212 - 174
112AAUU(chain B and (resid -3 through 17 or resid 22 through 33))BB-3 - 171 - 21
122UUAA(chain B and (resid -3 through 17 or resid 22 through 33))BB22 - 3326 - 37
212AAUU(chain D and (resid -3 through 17 or resid 22 through 33))DD-3 - 171 - 21
222UUAA(chain D and (resid -3 through 17 or resid 22 through 33))DD22 - 3326 - 37
312AAUU(chain F and (resid -3 through 17 or resid 22 through 33))FF-3 - 171 - 21
322UUAA(chain F and (resid -3 through 17 or resid 22 through 33))FF22 - 3326 - 37
412AAUU(chain H and (resid -3 through 17 or resid 22 through 33))HH-3 - 171 - 21
422UUAA(chain H and (resid -3 through 17 or resid 22 through 33))HH22 - 3326 - 37
512AAUU(chain J and (resid -3 through 17 or resid 22 through 33))JJ-3 - 171 - 21
522UUAA(chain J and (resid -3 through 17 or resid 22 through 33))JJ22 - 3326 - 37
612AAUU(chain L and (resid -3 through 17 or resid 22 through 33))LL-3 - 171 - 21
622UUAA(chain L and (resid -3 through 17 or resid 22 through 33))LL22 - 3326 - 37

NCS ensembles :
ID
1
2

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Components

#1: Protein
Type III toxin-antitoxin system ToxN/AbiQ family toxin


Mass: 21771.965 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DMO02_27240 / Variant: 680 BN4 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: RNA chain
Antitoxin RNA


Mass: 11844.016 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Variant: 680 BN4 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence of the protein has been deposited to NCBI with accession number WP_059274511.1 (GenBank ...Sequence of the protein has been deposited to NCBI with accession number WP_059274511.1 (GenBank OJR04057.1/UniParc: UPI000743281B).

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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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M disodium succinate pH 5.5, 0.02M MgCl2, 0.0015M spermidine, 2.4M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.097→43.94 Å / Num. obs: 104879 / % possible obs: 97.7 % / Redundancy: 3.471 % / CC1/2: 0.993 / Net I/σ(I): 3.53
Reflection shellResolution: 2.097→2.107 Å / Num. unique obs: 16559 / CC1/2: 0.517

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xdb

2xdb


Resolution: 2.097→43.297 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 2096 2 %
Rwork0.2128 102452 -
obs0.2132 104548 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.02 Å2 / Biso mean: 36.6376 Å2 / Biso min: 14.77 Å2
Refinement stepCycle: final / Resolution: 2.097→43.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7905 4584 0 498 12987
Biso mean---32.54 -
Num. residues----1200
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2748X-RAY DIFFRACTION1.419TORSIONAL
12C2748X-RAY DIFFRACTION1.419TORSIONAL
13E2748X-RAY DIFFRACTION1.419TORSIONAL
14G2748X-RAY DIFFRACTION1.419TORSIONAL
15I2748X-RAY DIFFRACTION1.419TORSIONAL
16K2748X-RAY DIFFRACTION1.419TORSIONAL
21B2268X-RAY DIFFRACTION1.419TORSIONAL
22D2268X-RAY DIFFRACTION1.419TORSIONAL
23F2268X-RAY DIFFRACTION1.419TORSIONAL
24H2268X-RAY DIFFRACTION1.419TORSIONAL
25J2268X-RAY DIFFRACTION1.419TORSIONAL
26L2268X-RAY DIFFRACTION1.419TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.097-2.14540.3431290.309633592
2.1454-2.19910.30541420.3026693899
2.1991-2.25850.39211370.3626672797
2.2585-2.3250.30541380.2868676397
2.325-2.40.2781370.2745667596
2.4-2.48580.29521410.2707688799
2.4858-2.58530.25981420.2638692499
2.5853-2.7030.27681420.2529694099
2.703-2.84540.28681410.246692799
2.8454-3.02370.29631420.2342694099
3.0237-3.25710.22791420.2189693099
3.2571-3.58470.22051370.195671096
3.5847-4.10310.20131430.1692697799
4.1031-5.16810.15431430.1466699099
5.1681-43.2970.16011400.1601678994
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)
14.18550.1690.87652.47270.08452.4516-0.12740.34640.2606-0.12090.1076-0.0336-0.14420.01280.00740.169-0.03170.03060.2170.03120.225539.48629.76734.95
20.76331.0153-1.2253.2562-2.38582.50250.1580.0960.12780.09810.07530.114-0.159-0.0467-0.21030.2861-0.04670.00990.2811-0.01690.232828.4514.2556.82
31.91440.84420.42422.98421.06892.24680.0377-0.0262-0.0260.1383-0.17490.18150.0275-0.20710.13280.2508-0.01430.00990.2335-0.03410.196215.634-8.08266.461
42.8344-0.8859-3.8360.49911.20892.9167-0.1149-0.0057-0.12650.1354-0.02410.03940.1564-0.01710.09070.2560.0640.00070.3518-0.01490.244434.324-21.08548.789
52.0932-0.32530.42833.0344-1.3912.70520.00560.09170.0903-0.4468-0.00170.00640.1481-0.04580.0060.28030.0169-0.01450.17340.00140.225146.886-22.7224.356
6-0.6698-0.3182-0.32415.93311.45110.4896-0.0101-0.02580.0729-0.45580.1642-0.33870.0090.0609-0.14290.2717-0.0068-0.00210.2437-0.04240.403550.1595.79127.625
73.81750.7031-0.80141.7726-0.07941.79720.1269-0.15810.25750.0067-0.05920.0154-0.25920.0376-0.03340.21140.02520.02620.1607-0.02870.2041.10328.62229.879
80.7804-1.2018-1.52373.60093.55553.53830.17550.14950.1466-0.2133-0.0764-0.035-0.2751-0.0537-0.08050.29610.03680.01840.29360.00470.216911.84514.4817.186
92.3665-0.91870.60432.3518-0.35232.7710.11360.1634-0.0426-0.1047-0.1583-0.1380.16710.15970.05510.21110.0078-0.00510.23140.01540.141624.569-7.342-3.143
102.87591.0653-3.51030.4018-1.19883.4346-0.23470.0876-0.2274-0.1847-0.0366-0.0860.3175-0.12090.19290.2825-0.03090.0110.2937-0.01090.23516.977-21.88614.45
112.08930.07750.41571.890.62813.34090.0373-0.0275-0.09990.08340.0117-0.11550.3003-0.0736-0.03720.2371-0.04160.01340.1566-0.02050.2093-5.358-24.70138.73
12-0.14310.3019-0.08015.9806-1.86280.83060.02860.0822-0.02730.3405-0.02620.21110.0067-0.0772-0.03290.22570.01080.04270.2592-0.05260.324-9.0943.93936.116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:162 )A0 - 162
2X-RAY DIFFRACTION2( CHAIN B AND RESID -3:33 )B-3 - 33
3X-RAY DIFFRACTION3( CHAIN C AND RESID 0:162 )C0 - 162
4X-RAY DIFFRACTION4( CHAIN D AND RESID -3:33 )D-3 - 33
5X-RAY DIFFRACTION5( CHAIN E AND RESID 0:162 )E0 - 162
6X-RAY DIFFRACTION6( CHAIN F AND RESID -3:33 )F-3 - 33
7X-RAY DIFFRACTION7( CHAIN G AND RESID 0:162 )G0 - 162
8X-RAY DIFFRACTION8( CHAIN H AND RESID -3:33 )H-3 - 33
9X-RAY DIFFRACTION9( CHAIN I AND RESID 0:162 )I0 - 162
10X-RAY DIFFRACTION10( CHAIN J AND RESID -3:33 )J-3 - 33
11X-RAY DIFFRACTION11( CHAIN K AND RESID 0:162 )K0 - 162
12X-RAY DIFFRACTION12( CHAIN L AND RESID -3:33 )L-3 - 33

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