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- PDB-6gts: Structure of the AtaT-AtaR complex bound DNA -

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Basic information

Entry
Database: PDB / ID: 6gts
TitleStructure of the AtaT-AtaR complex bound DNA
Components
  • Acetyltransferase
  • DNA
  • DUF1778 domain-containing protein
KeywordsTRANSCRIPTION / TA toxin / antitoxin / N-acetyl transferase / ribbon-helix-helix / RHH / bacterial repressor / toxin-antitoxin complex / protein-nucleic acid complex
Function / homology
Function and homology information


toxin sequestering activity / acyltransferase activity, transferring groups other than amino-acyl groups / regulation of DNA-templated transcription
Similarity search - Function
Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / Acetyltransferase (GNAT) domain / Ribbon-helix-helix / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
DNA / DNA (> 10) / GNAT family N-acetyltransferase / DUF1778 domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.357 Å
AuthorsGarcia-Pino, A. / Jurenas, D.
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Mechanism of regulation and neutralization of the AtaR-AtaT toxin-antitoxin system.
Authors: Jurenas, D. / Van Melderen, L. / Garcia-Pino, A.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Acetyltransferase
B: DUF1778 domain-containing protein
C: DUF1778 domain-containing protein
D: DNA


Theoretical massNumber of molelcules
Total (without water)46,3184
Polymers46,3184
Non-polymers00
Water00
1
A: Acetyltransferase
B: DUF1778 domain-containing protein
C: DUF1778 domain-containing protein
D: DNA

A: Acetyltransferase
B: DUF1778 domain-containing protein
C: DUF1778 domain-containing protein
D: DNA


Theoretical massNumber of molelcules
Total (without water)92,6358
Polymers92,6358
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_855-x+3,y,-z+1/21
Buried area19190 Å2
ΔGint-137 kcal/mol
Surface area37260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.729, 87.920, 190.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acetyltransferase / GNAT family N-acetyltransferase / N-acetyltransferase / N-acetyltransferase GCN5


Mass: 19716.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: A8G17_04180, ARC77_13660, AU473_04480, B7C53_02435, BTQ04_07045, ERS085404_01503
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0K4I8K2
#2: Protein DUF1778 domain-containing protein / Toxin-antitoxin system / antitoxin component / ribbon-helix-helix fold protein / Ybl13


Mass: 9925.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ybl13, ybl13_1, A8G17_04185, AA102_09360, AC789_1c38270, ACN002_3543, ACN81_27750, ACU90_15595, AM270_07745, ARC77_13665, AU473_04475, B1K96_23180, B1K96_30445, BHS81_20640, BIZ41_06975, BK292_ ...Gene: ybl13, ybl13_1, A8G17_04185, AA102_09360, AC789_1c38270, ACN002_3543, ACN81_27750, ACU90_15595, AM270_07745, ARC77_13665, AU473_04475, B1K96_23180, B1K96_30445, BHS81_20640, BIZ41_06975, BK292_07330, BMT53_16880, BN17_33961, BTQ04_07040, BWP17_00645, COD46_18440, CR538_01655, CVH05_12360, ERS085366_00076, ERS085374_01548, ERS085383_01733, ERS085404_01502, RX35_03224
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J7QA90
#3: DNA chain DNA


Mass: 6750.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) 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: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine, 10%(w/v) PEG 20 000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.357→95.24 Å / Num. obs: 7075 / % possible obs: 91 % / Redundancy: 7.3 % / Biso Wilson estimate: 170.64 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.9
Reflection shellResolution: 3.357→3.64 Å / Rmerge(I) obs: 0.863 / CC1/2: 0.352

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3161: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.357→42.834 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 42.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2887 306 5.34 %RANDOM
Rwork0.2636 ---
obs0.2649 5729 60.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.357→42.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 448 0 0 2578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032661
X-RAY DIFFRACTIONf_angle_d0.7253716
X-RAY DIFFRACTIONf_dihedral_angle_d19.9321517
X-RAY DIFFRACTIONf_chiral_restr0.038443
X-RAY DIFFRACTIONf_plane_restr0.004409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3574-4.22940.40071010.30811827X-RAY DIFFRACTION42
4.2294-42.83760.27072050.25583596X-RAY DIFFRACTION79
Refinement TLS params.Method: refined / Origin x: 105.672 Å / Origin y: 111.3085 Å / Origin z: 33.4108 Å
111213212223313233
T0.6465 Å20.4031 Å2-0.4144 Å2-0.8778 Å2-0.1317 Å2--0.7495 Å2
L2.1061 °20.4927 °2-0.6075 °2-2.9818 °20.4604 °2--3.6523 °2
S0.0837 Å °0.4798 Å °-0.1234 Å °-0.3834 Å °-0.4121 Å °0.3431 Å °-0.2296 Å °-0.4162 Å °0.2855 Å °
Refinement TLS groupSelection details: all

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