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- PDB-6gtp: Structure of the AtaT Y144F mutant toxin -

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Basic information

Entry
Database: PDB / ID: 6gtp
TitleStructure of the AtaT Y144F mutant toxin
ComponentsN-acetyltransferase
KeywordsTRANSCRIPTION / TA toxin / N-acetyl transferase / ribbon-helix-helix / RHH / bacterial repressor
Function / homologyAcetyltransferase (GNAT) domain / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / N-acetyltransferase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8925
Polymers21,9871
Non-polymers9054
Water75742
1
A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,78310
Polymers43,9742
Non-polymers1,8108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area4570 Å2
ΔGint-79 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.102, 58.102, 216.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein N-acetyltransferase /


Mass: 21986.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BWP17_00640, CVH05_12355
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1V3CQ74
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M calcium acetate hydrate, 0.1 M sodium acetate, 10%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.49→49.01 Å / Num. obs: 8089 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 62.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.2
Reflection shellResolution: 2.51→2.55 Å / Rmerge(I) obs: 1.52 / CC1/2: 0.448 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FVJ

5fvj


Resolution: 2.5→49.01 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.535 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.799 / SU Rfree Blow DPI: 0.309 / SU Rfree Cruickshank DPI: 0.298
RfactorNum. reflection% reflectionSelection details
Rfree0.254 372 5.15 %RANDOM
Rwork0.196 ---
obs0.199 7226 88.3 %-
Displacement parametersBiso mean: 62.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.0141 Å20 Å20 Å2
2---0.0141 Å20 Å2
3---0.0281 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.5→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 54 42 1471
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011463HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.271997HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d478SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes243HARMONIC5
X-RAY DIFFRACTIONt_it1463HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion20.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion193SEMIHARMONIC5
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_contact1687SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.8 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2725 -5.26 %
Rwork0.2237 1224 -
all0.2264 1292 -
obs--57.55 %
Refinement TLS params.Method: refined / Origin x: 5.9802 Å / Origin y: 18.2011 Å / Origin z: 116.481 Å
111213212223313233
T-0.112 Å2-0.0217 Å20.0236 Å2--0.0422 Å20.0093 Å2---0.1423 Å2
L3.6697 °20.7901 °2-0.2521 °2-2.2736 °2-0.4865 °2--2.722 °2
S-0.0333 Å °0.0689 Å °-0.2664 Å °0.1144 Å °0.0511 Å °0.0563 Å °0.2019 Å °-0.0513 Å °-0.0178 Å °
Refinement TLS groupSelection details: { A|* }

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