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- PDB-6g96: Crystal structure of TacT3 (tRNA acetylating toxin) from Salmonella -

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Basic information

Entry
Database: PDB / ID: 6g96
TitleCrystal structure of TacT3 (tRNA acetylating toxin) from Salmonella
ComponentsAcetyltransferase
KeywordsTRANSFERASE / Acetyltransferase / Toxin
Function / homologyacyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / Acetyltransferase / Acetyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47660774104 Å
AuthorsGrabe, G.J. / Rycroft, J.A. / Gollan, B. / Hall, A. / Cheverton, A.M. / Larrouy-Maumus, G. / Hare, S.A. / Helaine, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Activity of acetyltransferase toxins involved in Salmonella persister formation during macrophage infection.
Authors: Rycroft, J.A. / Gollan, B. / Grabe, G.J. / Hall, A. / Cheverton, A.M. / Larrouy-Maumus, G. / Hare, S.A. / Helaine, S.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Acetyltransferase
A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1487
Polymers38,1822
Non-polymers1,9675
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-15 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.786, 71.202, 86.313
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Acetyltransferase / N-acetyltransferase


Mass: 19090.840 Da / Num. of mol.: 2 / Mutation: Y143F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: CU490_09610, CX046_09695, DD95_05355 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J5HSJ5, UniProt: Q7CPW9*PLUS
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M Bicine 10% PEG 6000 0.25M NaCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cold nitrogen gas stream
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.47→86.31 Å / Num. obs: 67592 / % possible obs: 99.77 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.395192247 Å2 / Rpim(I) all: 0.094 / Net I/σ(I): 8.7
Reflection shellResolution: 1.48→1.5 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3298 / CC1/2: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
autoPROCdata scaling
PHASERphasing
Cootmodel building
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FVJ

5fvj


Resolution: 1.47660774104→54.925264675 Å / SU ML: 0.166119938097 / Cross valid method: FREE R-VALUE / σ(F): 1.35391799626 / Phase error: 25.4028116137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235338223391 3371 4.99629464947 %
Rwork0.208377236705 64099 -
obs0.209747103769 67470 99.7722701999 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.5448544237 Å2
Refinement stepCycle: LAST / Resolution: 1.47660774104→54.925264675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 125 460 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063447594282970
X-RAY DIFFRACTIONf_angle_d1.058353736124044
X-RAY DIFFRACTIONf_chiral_restr0.0676587566405439
X-RAY DIFFRACTIONf_plane_restr0.00458844266433514
X-RAY DIFFRACTIONf_dihedral_angle_d9.357314032761654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4766-1.49770.2766189051571370.2873905102592591X-RAY DIFFRACTION99.8901501282
1.4977-1.52010.3315184577341290.276191084332659X-RAY DIFFRACTION99.6426018585
1.5201-1.54380.3185426823661410.264605256722652X-RAY DIFFRACTION99.75
1.5438-1.56910.3166659970351470.2590878401512606X-RAY DIFFRACTION99.6741491673
1.5691-1.59620.2860604047491430.2452769604922646X-RAY DIFFRACTION99.8210450966
1.5962-1.62520.2140117970391280.2460849733982655X-RAY DIFFRACTION99.8923187365
1.6252-1.65650.2726516845351490.2325253789412644X-RAY DIFFRACTION99.8213009292
1.6565-1.69030.2750356990521540.2187431421832621X-RAY DIFFRACTION99.7842502697
1.6903-1.7270.2441950474521260.2204202790022654X-RAY DIFFRACTION99.892202659
1.727-1.76720.2141526569911280.2079969009382648X-RAY DIFFRACTION99.748472871
1.7672-1.81140.240893008851370.2089550335632660X-RAY DIFFRACTION99.7503566334
1.8114-1.86040.2672375701951520.2046643820852649X-RAY DIFFRACTION99.8930099857
1.8604-1.91510.2243529637561600.2032719661852631X-RAY DIFFRACTION99.7498213009
1.9151-1.9770.2425070758111420.2089427554712656X-RAY DIFFRACTION99.8216196932
1.977-2.04760.2421293908821210.2044338517552688X-RAY DIFFRACTION99.6452642781
2.0476-2.12960.1936789077231310.2011353000462657X-RAY DIFFRACTION99.7495527728
2.1296-2.22650.2195528225311240.1885866967552704X-RAY DIFFRACTION99.7179125529
2.2265-2.34390.2262141413761500.1975010349182669X-RAY DIFFRACTION99.8583067659
2.3439-2.49080.2375012023871380.2091815484212694X-RAY DIFFRACTION99.8941798942
2.4908-2.68310.2504520278391430.2051688795952680X-RAY DIFFRACTION99.8938428875
2.6831-2.95310.2265733323561240.2019206200432733X-RAY DIFFRACTION99.7207678883
2.9531-3.38030.2403621561641510.1938764838682703X-RAY DIFFRACTION99.9649737303
3.3803-4.25860.2082321683881490.1911245459042745X-RAY DIFFRACTION99.8275267334
4.2586-54.96330.2259986292931670.2142497896952854X-RAY DIFFRACTION99.1792514773

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