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- PDB-6m6u: Crystal structure the toxin-antitoxin MntA-HpeT mutant-D39ED41E -

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Basic information

Entry
Database: PDB / ID: 6m6u
TitleCrystal structure the toxin-antitoxin MntA-HpeT mutant-D39ED41E
Components
  • Toxin-antitoxin system antitoxin MntA 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: 2.349 Å
AuthorsOuyang, S.Y. / Zhen, X.K.
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 1.2Nov 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 antitoxin MntA 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 antitoxin MntA 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)123,2058
Polymers123,2058
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15230 Å2
ΔGint-35 kcal/mol
Surface area44670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.217, 99.954, 131.798
Angle α, β, γ (deg.)90.000, 96.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Toxin-antitoxin system antitoxin MntA family


Mass: 15610.635 Da / Num. of mol.: 2 / Mutation: D39E, D41E
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.: 6
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

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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: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30%(v/v)Jeffamine M-600 PH7.0 100mM HEPES/Sodium hydroxide PH7.0
PH range: 5-9

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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: 2.349→100.1 Å / Num. obs: 65138 / % possible obs: 99.74 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.21 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.6
Reflection shellResolution: 2.349→2.41 Å / Num. unique obs: 4450 / CC1/2: 0.744

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Processing

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

5yep


Resolution: 2.349→53.908 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1912 3.47 %
Rwork0.2041 53226 -
obs0.2051 55138 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.86 Å2 / Biso mean: 66.5052 Å2 / Biso min: 26.74 Å2
Refinement stepCycle: final / Resolution: 2.349→53.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8242 0 0 0 8242
Num. residues----1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048345
X-RAY DIFFRACTIONf_angle_d0.66811277
X-RAY DIFFRACTIONf_chiral_restr0.0481339
X-RAY DIFFRACTIONf_plane_restr0.0041475
X-RAY DIFFRACTIONf_dihedral_angle_d14.5125145
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.349-2.40740.37031140.2933327582
2.4074-2.47250.35241290.2903350187
2.4725-2.54530.34081260.2698352789
2.5453-2.62740.29971320.2555364491
2.6274-2.72130.26021340.2602369892
2.7213-2.83030.3111390.254377895
2.8303-2.95910.29321350.2557384896
2.9591-3.11510.27391410.2572389797
3.1151-3.31020.2941410.2463395598
3.3102-3.56580.27421430.2297399199
3.5658-3.92450.23631440.1953398599
3.9245-4.49210.191450.1692402499
4.4921-5.65860.21021440.17544019100
5.6586-53.9080.15781450.156408499
Refinement TLS params.Method: refined / Origin x: 20.0011 Å / Origin y: 9.053 Å / Origin z: 30.5326 Å
111213212223313233
T0.2378 Å2-0.0036 Å2-0.032 Å2-0.3123 Å20.0098 Å2--0.3457 Å2
L0.1218 °20.0563 °2-0.1308 °2-0.6469 °2-0.3041 °2--0.9093 °2
S-0.0301 Å °-0.0122 Å °-0.0778 Å °-0.1086 Å °0.0047 Å °0.0373 Å °0.1015 Å °-0.0823 Å °0.0001 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 DIFFRACTION1allF4 - 127
6X-RAY DIFFRACTION1allG2 - 131
7X-RAY DIFFRACTION1allH3 - 133
8X-RAY DIFFRACTION1allI2 - 133

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