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- PDB-5fvj: Crystal structure of TacT (tRNA acetylating toxin) from Salmonella -

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Basic information

Entry
Database: PDB / ID: 5fvj
TitleCrystal structure of TacT (tRNA acetylating toxin) from Salmonella
ComponentsPUTATIVE ACETYLTRANSFERASE
KeywordsTRANSFERASE / ACETYLTRANSFERASE
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
Similarity search - Function
Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Acetyltransferase / Acetyltransferase
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsPrzydacz, M. / Wong, C.T. / Cheverton, A.M. / Gollan, B. / Mylona, A. / Helaine, S. / Hare, S.A.
CitationJournal: Mol.Cell / Year: 2016
Title: A Salmonella Toxin Promotes Persister Formation Through Acetylation of tRNA.
Authors: Cheverton, A.M. / Gollan, B. / Przydacz, M. / Wong, C.T. / Mylona, A. / Hare, S.A. / Helaine, S.
History
DepositionFeb 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE ACETYLTRANSFERASE
B: PUTATIVE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8494
Polymers36,2302
Non-polymers1,6192
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-16.7 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.400, 85.660, 55.320
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 4 - 159 / Label seq-ID: 9 - 164

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein PUTATIVE ACETYLTRANSFERASE / TACT


Mass: 18114.846 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: E8XFW6, UniProt: Q8ZL98*PLUS
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.19 Å3/Da / Density % sol: 43.8 % / Description: NONE
Crystal growpH: 6.5
Details: 22 % (W/V) PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), 100 MM BIS-TRIS PH6.5, 50 MM AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.7→55.2 Å / Num. obs: 32830 / % possible obs: 96.2 % / Observed criterion σ(I): -4 / Redundancy: 6.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→55.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.044 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1676 5.1 %RANDOM
Rwork0.17164 ---
obs0.17447 30992 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20.24 Å2
2---0.63 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 102 426 3019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192727
X-RAY DIFFRACTIONr_bond_other_d0.0050.022657
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9963725
X-RAY DIFFRACTIONr_angle_other_deg1.20536098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39723.39118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82315451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4051520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213079
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02655
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4431.5121318
X-RAY DIFFRACTIONr_mcbond_other1.4141.5071315
X-RAY DIFFRACTIONr_mcangle_it1.5812.2521648
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9061.9431409
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.0135384
X-RAY DIFFRACTIONr_sphericity_free17.7235117
X-RAY DIFFRACTIONr_sphericity_bonded4.86955625
Refine LS restraints NCS

Ens-ID: 1 / Number: 17664 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 121 -
Rwork0.249 2322 -
obs--96.22 %

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