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- PDB-6m6v: Crystal structure the toxin-antitoxin MntA-HepT -

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Basic information

Entry
Database: PDB / ID: 6m6v
TitleCrystal structure the toxin-antitoxin MntA-HepT
Components
  • RNA (5'-R(P*AP*AP*A)-3')
  • Toxin-antitoxin system antidote Mnt family
  • Toxin-antitoxin system toxin HepN family
KeywordsANTITOXIN / crystal structure of a unique toxin-antitoxin system
Function / homology
Function and homology information


protein adenylyltransferase / toxin-antitoxin complex / RNA nuclease activity / nucleotidyltransferase activity / endonuclease activity / Hydrolases; Acting on ester bonds / nucleotide binding / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Polymerase beta, nucleotidyltransferase / Polymerase beta, Nucleotidyltransferase / Ribonuclease HepT-like / tRNA nuclease HepT-like superfamily / Ribonuclease HepT-like / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
RNA / mRNA nuclease HepT / Protein adenylyltransferase MntA
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsOuyang, S.Y. / Zhen, X.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Novel polyadenylylation-dependent neutralization mechanism of the HEPN/MNT toxin/antitoxin system.
Authors: Yao, J. / Zhen, X. / Tang, K. / Liu, T. / Xu, X. / Chen, Z. / Guo, Y. / Liu, X. / Wood, T.K. / Ouyang, S. / Wang, X.
History
DepositionMar 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Toxin-antitoxin system antidote Mnt family
B: Toxin-antitoxin system toxin HepN family
C: Toxin-antitoxin system toxin HepN family
D: Toxin-antitoxin system toxin HepN family
E: RNA (5'-R(P*AP*AP*A)-3')
F: RNA (5'-R(P*AP*AP*A)-3')
G: RNA (5'-R(P*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)64,4027
Polymers64,4027
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.560, 225.700, 52.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Toxin-antitoxin system antidote Mnt family


Mass: 15582.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: SO_3165 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ECH7
#2: Protein Toxin-antitoxin system toxin HepN family


Mass: 15330.544 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: SO_3166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ECH6
#3: RNA chain RNA (5'-R(P*AP*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 % (w/v) PEG 3350, 0.1M Magnesium acetate, 0.1M HEPS pH 7.0
PH range: 6.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97982 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97982 Å / Relative weight: 1
ReflectionResolution: 3.08→112.85 Å / Num. obs: 13153 / % possible obs: 99.25 % / Redundancy: 12.5 % / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 3.08→3.16 Å / Num. unique obs: 4214 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YEP

5yep


Resolution: 3.08→112.85 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.92
RfactorNum. reflection% reflection
Rfree0.2769 605 4.62 %
Rwork0.2208 --
obs0.2231 13093 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 230.92 Å2 / Biso mean: 84.6703 Å2 / Biso min: 39.88 Å2
Refinement stepCycle: final / Resolution: 3.08→112.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4118 198 0 0 4316
Num. residues----522
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0801-3.39010.38741740.3074300699
3.3901-3.88060.29461160.2463309299
3.8806-4.88920.25261500.1933113100
4.8892-112.850.25651650.2064327799
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)
14.5865-3.96050.55093.6721-1.23438.8102-0.1468-0.39370.20320.57720.3788-0.25670.2476-0.0662-0.09210.62030.0371-0.06340.5139-0.06741.106518.919715.02520.9867
25.31542.1417-0.80376.8984-1.88161.75360.14960.2323-0.8216-0.20830.19230.6567-0.1696-0.01160.16450.60570.00980.06280.4817-0.03091.18419.49069.303311.3275
34.2736-0.16090.47486.0556-2.87851.35250.0153-0.32820.34340.53620.10910.942-0.0589-0.4119-0.02230.56410.0711-0.0740.565-0.00011.083613.028619.873916.1808
46.92810.94424.39715.9551-0.72415.1464-0.4193-0.4910.70520.00790.11860.9702-0.3148-0.49230.34240.48430.04780.04220.5043-0.06271.14525.763431.11769.5281
58.82111.7397-3.52684.3482-5.97677.96230.0717-0.5009-0.2856-0.4287-1.2522-1.82780.68680.87231.38450.5515-0.0843-0.00150.569-0.07611.231721.109649.91289.1952
63.31422.4174-4.15544.8933-4.60828.487-0.210.0341-0.31120.31160.1504-0.681-0.1936-0.3530.10480.50930.0485-0.02170.53510.02381.171712.130846.93846.1535
72.3941-1.343-0.21074.1346-3.78547.9257-0.01740.0729-0.01980.31420.4050.5387-0.2244-0.8028-0.32650.4059-0.02360.04690.6168-0.08521.14984.098250.46637.744
88.0028-3.02224.12273.8959-3.90374.0687-1.1119-0.39841.01371.24390.35420.4104-1.2534-0.50550.98160.6575-0.0803-0.05570.5126-0.13630.630114.145453.409417.4557
97.09281.84731.88333.9044-0.35951.4935-0.98010.02730.915-0.71270.2961-0.0293-0.51220.02590.49151.00220.0604-0.08710.5442-0.01150.22248.28140.551-15.5065
107.5039-0.0595-4.78982.12761.16475.01770.3514-0.1916-0.5251-1.333-1.2933-1.7219-1.48410.78380.88570.78140.10370.06760.6917-0.04811.293229.407845.7219-11.8689
117.38814.5611-2.91253.9331-1.39171.5107-0.48610.5428-0.2667-0.81160.26660.13370.2808-0.45470.210.4977-0.0263-0.07560.6096-0.07980.83057.191734.1465-5.7651
122.10420.731-3.27682.6646-0.33428.5058-0.97480.6411-2.43320.42321.1836-0.15491.97020.2437-0.30150.8137-0.12650.07130.6554-0.10051.32475.479620.8447-7.4806
138.73281.36550.1718.547-0.20496.52460.02910.1784-2.04050.35970.07540.08960.71190.2025-0.00740.62040.07210.0660.5388-0.03510.667814.398728.6843-4.6261
149.5498-1.4154-1.66687.2999-1.7368.14680.33330.0084-0.6792-0.2307-0.1015-1.99810.8721.03440.30520.50030.05020.01490.45990.06091.131823.900134.4207-5.2483
155.09073.15554.63022.55612.60924.37221.6840.7968-1.1722-0.3338-0.03150.19871.7737-0.6877-1.71561.2918-0.3072-0.19410.85660.02970.70968.154129.5081-17.7387
165.44152.93012.17095.23756.93619.5388-0.2320.0970.1274-0.25230.555-1.04530.18260.3322-0.33880.606-0.0215-0.00280.63420.22761.1731-6.239213.52542.1433
173.057-1.215-3.10021.82432.97897.55570.0094-0.28670.358-0.09860.363-0.2791-0.35950.4747-0.37650.6130.06340.01030.441-0.03711.1687-9.6996.950310.7106
182.89181.0076-4.15773.10780.83669.4579-0.533-1.53960.25830.93820.1587-1.30190.78930.86350.34610.60930.0982-0.21070.61530.03011.2722-14.021.77211.8872
194.15973.9601-0.06129.94577.73229.77760.1405-0.1410.16750.47780.2137-0.15940.4124-0.0501-0.08870.5146-0.08040.05240.52440.09760.688-11.7508-6.63841.4184
203.06710.1173-0.70326.01724.85634.114-0.09540.39460.7208-0.41010.07110.0184-0.4433-0.90390.45460.64110.0466-0.06260.58790.04271.8581-16.074314.13427.2106
215.67432.7728-0.61213.5572-2.98573.3866-0.09530.3052-0.2502-2.7752-0.4257-2.4780.1768-1.76110.57521.03150.07950.33090.7767-0.00421.5305-1.070952.62382.2409
224.9957-4.384-2.86097.6184.19018.09980.34970.641-0.1286-0.68020.1845-1.03230.76290.2288-0.53810.71660.05310.00550.68890.01391.404422.001628.2129-0.7784
239.4254-3.1626-7.25823.56882.82246.4734-0.6345-2.72020.3508-0.00211.9306-0.3171-1.85580.9893-0.19211.37260.14170.66511.89030.55362.8757-5.0741-15.430316.5536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 46 )A2 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 66 )A47 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 96 )A67 - 96
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 127 )A97 - 127
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 23 )B2 - 23
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 68 )B24 - 68
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 119 )B69 - 119
8X-RAY DIFFRACTION8chain 'B' and (resid 120 through 133 )B120 - 133
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 23 )C2 - 23
10X-RAY DIFFRACTION10chain 'C' and (resid 24 through 32 )C24 - 32
11X-RAY DIFFRACTION11chain 'C' and (resid 33 through 69 )C33 - 69
12X-RAY DIFFRACTION12chain 'C' and (resid 70 through 83 )C70 - 83
13X-RAY DIFFRACTION13chain 'C' and (resid 84 through 102 )C84 - 102
14X-RAY DIFFRACTION14chain 'C' and (resid 103 through 119 )C103 - 119
15X-RAY DIFFRACTION15chain 'C' and (resid 120 through 133 )C120 - 133
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 23 )D2 - 23
17X-RAY DIFFRACTION17chain 'D' and (resid 24 through 83 )D24 - 83
18X-RAY DIFFRACTION18chain 'D' and (resid 84 through 101 )D84 - 101
19X-RAY DIFFRACTION19chain 'D' and (resid 102 through 118 )D102 - 118
20X-RAY DIFFRACTION20chain 'D' and (resid 119 through 133 )D119 - 133
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 3 )E1 - 3
22X-RAY DIFFRACTION22chain 'F' and (resid 1 through 3 )F1 - 3
23X-RAY DIFFRACTION23chain 'G' and (resid 1 through 3 )G1 - 3

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