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- PDB-7aer: Rebuilt and re-refined PDB entry 5yep: tri-AMPylated Shewanella o... -

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Basic information

Entry
Database: PDB / ID: 7aer
TitleRebuilt and re-refined PDB entry 5yep: tri-AMPylated Shewanella oneidensis HEPN toxin in complex with MNT antitoxin
Components
  • Toxin-antitoxin system antidote Mnt family
  • Toxin-antitoxin system toxin HepN family
KeywordsTOXIN/ANTITOXIN / toxin-antitoxin system / MNT-HEPN / AMPylation / TOXIN-ANTITOXIN complex
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
ADENOSINE MONOPHOSPHATE / mRNA nuclease HepT / Protein adenylyltransferase MntA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsTamulaitiene, G. / Sasnauskas, G. / Songailiene, I. / Juozapaitis, J. / Siksnys, V.
Citation
Journal: Mol.Cell / Year: 2020
Title: HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation.
Authors: Songailiene, I. / Juozapaitis, J. / Tamulaitiene, G. / Ruksenaite, A. / Sulcius, S. / Sasnauskas, G. / Venclovas, C. / Siksnys, V.
#1: Journal: J. Biol. Chem. / Year: 2018
Title: Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system.
Authors: Jia, X. / Yao, J. / Gao, Z. / Liu, G. / Dong, Y.H. / Wang, X. / Zhang, H.
History
DepositionSep 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,56610
Polymers64,4834
Non-polymers2,0836
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-6 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.610, 224.380, 53.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 112 through 130 or (resid 131...
21(chain C and (resid 112 through 120 or (resid 121...
31(chain D and (resid 112 through 120 or (resid 121...
12(chain B and ((resid 2 and (name N or name...
22(chain C and (resid 2 through 20 or (resid 21...
32(chain D and ((resid 2 and (name N or name...
13(chain B and (resid 81 through 90 or (resid 91...
23(chain C and resid 81 through 91)
33(chain D and (resid 81 through 90 or (resid 91...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resid 112 through 130 or (resid 131...B0
211(chain C and (resid 112 through 120 or (resid 121...C112 - 120
221(chain C and (resid 112 through 120 or (resid 121...C121
231(chain C and (resid 112 through 120 or (resid 121...C2 - 203
241(chain C and (resid 112 through 120 or (resid 121...C2 - 203
251(chain C and (resid 112 through 120 or (resid 121...C2 - 203
261(chain C and (resid 112 through 120 or (resid 121...C2 - 203
311(chain D and (resid 112 through 120 or (resid 121...D112 - 120
321(chain D and (resid 112 through 120 or (resid 121...D121
331(chain D and (resid 112 through 120 or (resid 121...D2 - 133
341(chain D and (resid 112 through 120 or (resid 121...D2 - 133
351(chain D and (resid 112 through 120 or (resid 121...D2 - 133
361(chain D and (resid 112 through 120 or (resid 121...D2 - 133
112(chain B and ((resid 2 and (name N or name...B2
122(chain B and ((resid 2 and (name N or name...B1 - 203
132(chain B and ((resid 2 and (name N or name...B1 - 203
142(chain B and ((resid 2 and (name N or name...B1 - 203
152(chain B and ((resid 2 and (name N or name...B1 - 203
212(chain C and (resid 2 through 20 or (resid 21...C2 - 20
222(chain C and (resid 2 through 20 or (resid 21...C21
232(chain C and (resid 2 through 20 or (resid 21...C2 - 203
242(chain C and (resid 2 through 20 or (resid 21...C2 - 203
252(chain C and (resid 2 through 20 or (resid 21...C2 - 203
262(chain C and (resid 2 through 20 or (resid 21...C2 - 203
312(chain D and ((resid 2 and (name N or name...D2
322(chain D and ((resid 2 and (name N or name...D2 - 133
332(chain D and ((resid 2 and (name N or name...D2 - 133
342(chain D and ((resid 2 and (name N or name...D2 - 133
352(chain D and ((resid 2 and (name N or name...D2 - 133
113(chain B and (resid 81 through 90 or (resid 91...B0
213(chain C and resid 81 through 91)C81 - 91
313(chain D and (resid 81 through 90 or (resid 91...D0

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Toxin-antitoxin system antidote Mnt family


Mass: 15723.268 Da / Num. of mol.: 1
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: 16253.215 Da / Num. of mol.: 3
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Bicine (pH 8.6), 14% PEG6000 and 8% Ethlene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14273 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.93
Reflection shellResolution: 3→3.08 Å / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 3.51 / Num. unique obs: 1031 / CC1/2: 0.949 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXphenix-1.12-2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3→48.15 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2725 711 4.98 %
Rwork0.2265 13559 -
obs0.2289 14270 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.29 Å2 / Biso mean: 72.3087 Å2 / Biso min: 31.41 Å2
Refinement stepCycle: final / Resolution: 3→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 132 0 4199
Biso mean--71.27 --
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024265
X-RAY DIFFRACTIONf_angle_d0.5525804
X-RAY DIFFRACTIONf_chiral_restr0.037693
X-RAY DIFFRACTIONf_plane_restr0.003735
X-RAY DIFFRACTIONf_dihedral_angle_d13.3162581
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B288X-RAY DIFFRACTION10.952TORSIONAL
12C288X-RAY DIFFRACTION10.952TORSIONAL
13D288X-RAY DIFFRACTION10.952TORSIONAL
21B800X-RAY DIFFRACTION10.952TORSIONAL
22C800X-RAY DIFFRACTION10.952TORSIONAL
23D800X-RAY DIFFRACTION10.952TORSIONAL
31B146X-RAY DIFFRACTION10.952TORSIONAL
32C146X-RAY DIFFRACTION10.952TORSIONAL
33D146X-RAY DIFFRACTION10.952TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3-3.23160.33411370.29892625
3.2316-3.55670.36211410.27842689
3.5567-4.07120.29011400.23622675
4.0712-5.12830.24141430.20762710
5.1283-48.150.24561500.20352860

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