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- PDB-6gto: Structure of the AtaR antitoxin -

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Basic information

Entry
Database: PDB / ID: 6gto
TitleStructure of the AtaR antitoxin
ComponentsDUF1778 domain-containing protein
KeywordsTRANSCRIPTION / antitoxin / transcription factor / ribbon-helix-helix / RHH / bacterial repressor
Function / homologyVibrio phage ICP1, Orf50 / Antitoxin TacA 1-like / toxin sequestering activity / Ribbon-helix-helix / regulation of DNA-templated transcription / DUF1778 domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 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 18, 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: DUF1778 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0175
Polymers9,9251
Non-polymers924
Water00
1
A: DUF1778 domain-containing protein
hetero molecules

A: DUF1778 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,03510
Polymers19,8512
Non-polymers1848
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area3260 Å2
ΔGint-81 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.000, 56.000, 165.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DUF1778 domain-containing protein / Toxin-antitoxin system / antitoxin component / ribbon-helix-helix fold protein / Ybl13


Mass: 9925.330 Da / Num. of mol.: 1
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
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na

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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: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 35%(v/v) 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.97→41.86 Å / Num. obs: 3575 / % possible obs: 99.61 % / Redundancy: 5.5 % / Biso Wilson estimate: 117.7 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.58
Reflection shellResolution: 2.97→3.08 Å / Rmerge(I) obs: 1.482 / CC1/2: 0.538 / % possible all: 99.42

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→41.86 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.4 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.283
RfactorNum. reflection% reflectionSelection details
Rfree0.266 179 5.01 %RANDOM
Rwork0.234 ---
obs0.236 3576 99.7 %-
Displacement parametersBiso mean: 134.29 Å2
Baniso -1Baniso -2Baniso -3
1--6.5855 Å20 Å20 Å2
2---6.5855 Å20 Å2
3---13.171 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: 1 / Resolution: 2.97→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms460 0 4 0 464
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01463HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2627HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d164SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes83HARMONIC5
X-RAY DIFFRACTIONt_it463HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.15
X-RAY DIFFRACTIONt_other_torsion19.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion69SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact537SEMIHARMONIC4
LS refinement shellResolution: 2.97→3.32 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.1966 -5.02 %
Rwork0.2439 927 -
all0.2414 976 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: 27.1228 Å / Origin y: 19.2179 Å / Origin z: 75.0485 Å
111213212223313233
T-0.3178 Å2-0.0151 Å2-0.0875 Å2--0.1738 Å2-0.2506 Å2---0.1698 Å2
L3.4063 °2-2.3868 °2-1.8529 °2-5.6282 °24.6728 °2--6.7246 °2
S0.2378 Å °-0.3887 Å °0.259 Å °-0.1912 Å °0.0201 Å °0.2071 Å °-0.031 Å °0.1693 Å °-0.2579 Å °
Refinement TLS groupSelection details: { A|* }

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