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- PDB-6m6w: Crystal structure the toxin-antitoxin MntA-HpeT mutant-Y104A -

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Basic information

Entry
Database: PDB / ID: 6m6w
TitleCrystal structure the toxin-antitoxin MntA-HpeT mutant-Y104A
Components
  • 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
mRNA nuclease HepT / Protein adenylyltransferase MntA
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.611 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 / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 28, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 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

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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
F: Toxin-antitoxin system antidote Mnt family
G: Toxin-antitoxin system toxin HepN family
H: Toxin-antitoxin system toxin HepN family
I: Toxin-antitoxin system toxin HepN family


Theoretical massNumber of molelcules
Total (without water)122,5968
Polymers122,5968
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)54.102, 100.819, 131.781
Angle α, β, γ (deg.)90.000, 97.090, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain I and (resseq 3:16 or resseq 19:27 or resseq...
21(chain B and (resseq 3:16 or resseq 19:27 or resseq...
31(chain C and (resseq 3:16 or resseq 19:27 or resseq...
41(chain D and (resseq 3:16 or resseq 19:27 or resseq...
51(chain H and (resseq 3:16 or resseq 19:27 or resseq...
12(chain A and (resseq 4:18 or resseq 20:30 or resseq...
22(chain F and (resseq 4:18 or resseq 20:30 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain I and (resseq 3:16 or resseq 19:27 or resseq...I3 - 16
121(chain I and (resseq 3:16 or resseq 19:27 or resseq...I19 - 27
131(chain I and (resseq 3:16 or resseq 19:27 or resseq...I29
141(chain I and (resseq 3:16 or resseq 19:27 or resseq...I32
151(chain I and (resseq 3:16 or resseq 19:27 or resseq...I45 - 58
161(chain I and (resseq 3:16 or resseq 19:27 or resseq...I60
171(chain I and (resseq 3:16 or resseq 19:27 or resseq...I62 - 61
181(chain I and (resseq 3:16 or resseq 19:27 or resseq...I85 - 91
191(chain I and (resseq 3:16 or resseq 19:27 or resseq...I90 - 97
1101(chain I and (resseq 3:16 or resseq 19:27 or resseq...I2 - 133
1111(chain I and (resseq 3:16 or resseq 19:27 or resseq...I109
1121(chain I and (resseq 3:16 or resseq 19:27 or resseq...I111 - 120
1131(chain I and (resseq 3:16 or resseq 19:27 or resseq...I0
1141(chain I and (resseq 3:16 or resseq 19:27 or resseq...I132
211(chain B and (resseq 3:16 or resseq 19:27 or resseq...B3 - 16
221(chain B and (resseq 3:16 or resseq 19:27 or resseq...B19 - 27
231(chain B and (resseq 3:16 or resseq 19:27 or resseq...B0
241(chain B and (resseq 3:16 or resseq 19:27 or resseq...B45 - 58
251(chain B and (resseq 3:16 or resseq 19:27 or resseq...B45 - 58
261(chain B and (resseq 3:16 or resseq 19:27 or resseq...B60
271(chain B and (resseq 3:16 or resseq 19:27 or resseq...B62 - 69
281(chain B and (resseq 3:16 or resseq 19:27 or resseq...B71 - 83
291(chain B and (resseq 3:16 or resseq 19:27 or resseq...B85 - 91
2101(chain B and (resseq 3:16 or resseq 19:27 or resseq...B93 - 97
2111(chain B and (resseq 3:16 or resseq 19:27 or resseq...B100
2121(chain B and (resseq 3:16 or resseq 19:27 or resseq...B109
2131(chain B and (resseq 3:16 or resseq 19:27 or resseq...B111 - 120
2141(chain B and (resseq 3:16 or resseq 19:27 or resseq...B122 - 130
2151(chain B and (resseq 3:16 or resseq 19:27 or resseq...B132
311(chain C and (resseq 3:16 or resseq 19:27 or resseq...C3 - 16
321(chain C and (resseq 3:16 or resseq 19:27 or resseq...C19 - 27
331(chain C and (resseq 3:16 or resseq 19:27 or resseq...C0
341(chain C and (resseq 3:16 or resseq 19:27 or resseq...C60
351(chain C and (resseq 3:16 or resseq 19:27 or resseq...C45
361(chain C and (resseq 3:16 or resseq 19:27 or resseq...C6271 - 83
371(chain C and (resseq 3:16 or resseq 19:27 or resseq...C85 - 91
381(chain C and (resseq 3:16 or resseq 19:27 or resseq...C2 - 133
391(chain C and (resseq 3:16 or resseq 19:27 or resseq...C100
3101(chain C and (resseq 3:16 or resseq 19:27 or resseq...C109120
3111(chain C and (resseq 3:16 or resseq 19:27 or resseq...C122 - 133
3121(chain C and (resseq 3:16 or resseq 19:27 or resseq...C0
3131(chain C and (resseq 3:16 or resseq 19:27 or resseq...C2 - 133
3141(chain C and (resseq 3:16 or resseq 19:27 or resseq...C132
411(chain D and (resseq 3:16 or resseq 19:27 or resseq...D3 - 16
421(chain D and (resseq 3:16 or resseq 19:27 or resseq...D19 - 27
431(chain D and (resseq 3:16 or resseq 19:27 or resseq...D29
441(chain D and (resseq 3:16 or resseq 19:27 or resseq...D45 - 58
451(chain D and (resseq 3:16 or resseq 19:27 or resseq...D60
461(chain D and (resseq 3:16 or resseq 19:27 or resseq...D45
471(chain D and (resseq 3:16 or resseq 19:27 or resseq...D83
481(chain D and (resseq 3:16 or resseq 19:27 or resseq...D0
491(chain D and (resseq 3:16 or resseq 19:27 or resseq...D2 - 133
4101(chain D and (resseq 3:16 or resseq 19:27 or resseq...D109 - 97
4111(chain D and (resseq 3:16 or resseq 19:27 or resseq...D111 - 120
4121(chain D and (resseq 3:16 or resseq 19:27 or resseq...D0
4131(chain D and (resseq 3:16 or resseq 19:27 or resseq...D2 - 133
4141(chain D and (resseq 3:16 or resseq 19:27 or resseq...D132
511(chain H and (resseq 3:16 or resseq 19:27 or resseq...H3 - 16
521(chain H and (resseq 3:16 or resseq 19:27 or resseq...H19 - 27
531(chain H and (resseq 3:16 or resseq 19:27 or resseq...H29
541(chain H and (resseq 3:16 or resseq 19:27 or resseq...H32
551(chain H and (resseq 3:16 or resseq 19:27 or resseq...H34 - 43
561(chain H and (resseq 3:16 or resseq 19:27 or resseq...H45 - 58
571(chain H and (resseq 3:16 or resseq 19:27 or resseq...H60
581(chain H and (resseq 3:16 or resseq 19:27 or resseq...H62 - 69
591(chain H and (resseq 3:16 or resseq 19:27 or resseq...H71 - 83
5101(chain H and (resseq 3:16 or resseq 19:27 or resseq...H85 - 91
5111(chain H and (resseq 3:16 or resseq 19:27 or resseq...H93 - 97
5121(chain H and (resseq 3:16 or resseq 19:27 or resseq...H100
5131(chain H and (resseq 3:16 or resseq 19:27 or resseq...H109
5141(chain H and (resseq 3:16 or resseq 19:27 or resseq...H111 - 120
5151(chain H and (resseq 3:16 or resseq 19:27 or resseq...H122 - 130
5161(chain H and (resseq 3:16 or resseq 19:27 or resseq...H132
112(chain A and (resseq 4:18 or resseq 20:30 or resseq...A4 - 18
122(chain A and (resseq 4:18 or resseq 20:30 or resseq...A20 - 30
132(chain A and (resseq 4:18 or resseq 20:30 or resseq...A39 - 97
142(chain A and (resseq 4:18 or resseq 20:30 or resseq...A0
152(chain A and (resseq 4:18 or resseq 20:30 or resseq...A4 - 127
162(chain A and (resseq 4:18 or resseq 20:30 or resseq...A4 - 127
172(chain A and (resseq 4:18 or resseq 20:30 or resseq...A4 - 127
182(chain A and (resseq 4:18 or resseq 20:30 or resseq...A4 - 127
192(chain A and (resseq 4:18 or resseq 20:30 or resseq...A4 - 127
1102(chain A and (resseq 4:18 or resseq 20:30 or resseq...A4 - 127
1112(chain A and (resseq 4:18 or resseq 20:30 or resseq...A4 - 127
212(chain F and (resseq 4:18 or resseq 20:30 or resseq...F4 - 18
222(chain F and (resseq 4:18 or resseq 20:30 or resseq...F20 - 30
232(chain F and (resseq 4:18 or resseq 20:30 or resseq...F39 - 97
242(chain F and (resseq 4:18 or resseq 20:30 or resseq...F0
252(chain F and (resseq 4:18 or resseq 20:30 or resseq...F3 - 127
262(chain F and (resseq 4:18 or resseq 20:30 or resseq...F3 - 127
272(chain F and (resseq 4:18 or resseq 20:30 or resseq...F3 - 127
282(chain F and (resseq 4:18 or resseq 20:30 or resseq...F3 - 127
292(chain F and (resseq 4:18 or resseq 20:30 or resseq...F3 - 127
2102(chain F and (resseq 4:18 or resseq 20:30 or resseq...F3 - 127
2112(chain F and (resseq 4:18 or resseq 20:30 or resseq...F3 - 127

NCS ensembles :
ID
1
2

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Components

#1: Protein Toxin-antitoxin system antidote Mnt family


Mass: 15582.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / 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: 15238.448 Da / Num. of mol.: 6 / Mutation: Y104A
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: SO_3166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ECH6

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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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 20%peg4000, 0.1 M HEPES,pH 7.5 / PH range: 7-10

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.61→79.85 Å / Num. obs: 286711 / % possible obs: 99.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 73 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.7
Reflection shellResolution: 2.61→2.75 Å / Num. unique obs: 41811 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
EPMRphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YEP

5yep


Resolution: 2.611→39.19 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 3910 4.71 %
Rwork0.2145 79058 -
obs0.2159 82968 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.82 Å2 / Biso mean: 92.0928 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.611→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8143 0 0 0 8143
Num. residues----1020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088233
X-RAY DIFFRACTIONf_angle_d1.10511120
X-RAY DIFFRACTIONf_chiral_restr0.061328
X-RAY DIFFRACTIONf_plane_restr0.0051453
X-RAY DIFFRACTIONf_dihedral_angle_d14.9085082
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11I2250X-RAY DIFFRACTION14.813TORSIONAL
12B2250X-RAY DIFFRACTION14.813TORSIONAL
13C2250X-RAY DIFFRACTION14.813TORSIONAL
14D2250X-RAY DIFFRACTION14.813TORSIONAL
15H2250X-RAY DIFFRACTION14.813TORSIONAL
21A1045X-RAY DIFFRACTION14.813TORSIONAL
22F1045X-RAY DIFFRACTION14.813TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6113-2.64320.37221350.3429283399
2.6432-2.67660.41311350.3154284499
2.6766-2.71180.36931270.3222280798
2.7118-2.7490.35231490.3064274898
2.749-2.78820.34121620.2812282299
2.7882-2.82990.29931350.2908280599
2.8299-2.87410.35591430.2812283999
2.8741-2.92120.29791280.293277399
2.9212-2.97150.35281470.2973287299
2.9715-3.02550.30821300.296287399
3.0255-3.08370.32191480.2898279599
3.0837-3.14660.32631340.2889283199
3.1466-3.2150.3381380.2836281799
3.215-3.28980.27621600.2669279999
3.2898-3.3720.32641540.27288099
3.372-3.46310.28441050.2683280599
3.4631-3.56490.30011660.2522284199
3.5649-3.67990.29521340.2386281999
3.6799-3.81130.25521380.2153280999
3.8113-3.96380.25321370.2181281399
3.9638-4.1440.24151400.2077284499
4.144-4.36220.21521450.1819281199
4.3622-4.63510.19171460.1757280099
4.6351-4.99240.18291440.18292878100
4.9924-5.49350.28061330.2041285799
5.4935-6.28570.22911240.2245281899
6.2857-7.90860.25351350.19432855100
7.9086-39.190.13351380.1335277097
Refinement TLS params.Method: refined / Origin x: 3.1189 Å / Origin y: 6.4344 Å / Origin z: 161.2684 Å
111213212223313233
T0.4479 Å2-0.0073 Å2-0.039 Å2-0.5063 Å20.0123 Å2--0.5914 Å2
L0.4109 °20.0887 °2-0.2674 °2-0.6806 °2-0.3326 °2--1.5939 °2
S-0.0432 Å °0.0016 Å °-0.0351 Å °-0.1216 Å °0.0579 Å °0.0539 Å °0.1637 Å °-0.1119 Å °-0.015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 127
2X-RAY DIFFRACTION1allB2 - 133
3X-RAY DIFFRACTION1allC2 - 133
4X-RAY DIFFRACTION1allD2 - 133
5X-RAY DIFFRACTION1allF3 - 127
6X-RAY DIFFRACTION1allG2 - 131
7X-RAY DIFFRACTION1allH3 - 133
8X-RAY DIFFRACTION1allI2 - 133

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