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- PDB-7bxo: Crystal structure of the toxin-antitoxin with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 7bxo
TitleCrystal structure of the toxin-antitoxin with AMP-PNP
Components
  • Toxin-antitoxin system antidote Mnt family
  • Toxin-antitoxin system toxin HepN family
KeywordsTOXIN / a novel 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / mRNA nuclease HepT / Protein adenylyltransferase MntA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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
DepositionApr 20, 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 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: Toxin-antitoxin system antidote Mnt family
F: Toxin-antitoxin system toxin HepN family
G: Toxin-antitoxin system toxin HepN family
H: Toxin-antitoxin system toxin HepN family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,70514
Polymers122,5968
Non-polymers1,1106
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-76 kcal/mol
Surface area44460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.510, 100.680, 132.510
Angle α, β, γ (deg.)90.000, 96.440, 90.000
Int Tables number4
Space group name H-MP1211

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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
Source: (gene. exp.) Shewanella oneidensis (strain 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
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: SO_3166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ECH6
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl , 0.2 M potassium sodium tartrate, and 12-20% (v/v) PEG 3350
PH range: pH 7.8-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.77→100.68 Å / Num. obs: 36307 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 94.42 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 2.77→2.86 Å / Num. unique obs: 2668 / CC1/2: 0.999 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.1refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YEP

5yep


Resolution: 2.77→36.14 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 1.035 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.8 / SU Rfree Blow DPI: 0.318 / SU Rfree Cruickshank DPI: 0.331
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1856 5.12 %RANDOM
Rwork0.215 ---
obs0.217 36247 99.8 %-
Displacement parametersBiso max: 172.96 Å2 / Biso mean: 86.49 Å2 / Biso min: 38.12 Å2
Baniso -1Baniso -2Baniso -3
1--9.239 Å20 Å2-7.3059 Å2
2---3.3902 Å20 Å2
3---12.6292 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.77→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8241 0 66 14 8321
Biso mean--89.39 66.05 -
Num. residues----1034
LS refinement shellResolution: 2.77→2.79 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3425 44 6.07 %
Rwork0.2746 681 -
all0.2787 725 -
obs--99.86 %

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