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- PDB-7f36: TacT complexed with acetyl-glycyl-tRNAGly -

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Basic information

Entry
Database: PDB / ID: 7f36
TitleTacT complexed with acetyl-glycyl-tRNAGly
Components
  • N-acetyltransferase domain-containing protein
  • RNA (76-MER)
KeywordsTRANSFERASE / Acetyltranferase / TOXIN
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / tRNA binding
Similarity search - Function
Acetyltransferase (GNAT) domain / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYLAMINO-ACETIC ACID / : / RNA / RNA (> 10) / tRNA-acetylating toxin 1
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.098 Å
AuthorsYashiro, Y. / Tomita, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)LS136 Japan
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)26113002 Japan
Japan Society for the Promotion of Science (JSPS)19K16069 Japan
CitationJournal: Cell Rep / Year: 2021
Title: Molecular basis of glycyl-tRNAGly acetylation by TacT from Salmonella Typhimurium
Authors: Yashiro, Y. / Zhang, C. / Sakaguchi, Y. / Suzuki, T. / Tomita, K.
History
DepositionJun 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein
F: RNA (76-MER)
D: N-acetyltransferase domain-containing protein
C: N-acetyltransferase domain-containing protein
G: RNA (76-MER)
H: RNA (76-MER)
E: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,94150
Polymers173,1818
Non-polymers1,76042
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-412 kcal/mol
Surface area74240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.743, 121.873, 127.257
Angle α, β, γ (deg.)90.000, 91.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 4 through 160)
21(chain B and resid 4 through 160)
31(chain C and resid 4 through 160)
41(chain D and resid 4 through 160)
12(chain E and resid 1 through 75)
22(chain F and (resid 1 through 33 or resid 37 through 75))
32(chain G and (resid 1 through 33 or resid 37 through 75))
42chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALPROPRO(chain A and resid 4 through 160)AA4 - 1604 - 160
211VALVALPROPRO(chain B and resid 4 through 160)BB4 - 1604 - 160
311VALVALPROPRO(chain C and resid 4 through 160)CE4 - 1604 - 160
411VALVALPROPRO(chain D and resid 4 through 160)DD4 - 1604 - 160
112GGCC(chain E and resid 1 through 75)EH1 - 751 - 75
212GGUU(chain F and (resid 1 through 33 or resid 37 through 75))FC1 - 331 - 33
222AACC(chain F and (resid 1 through 33 or resid 37 through 75))FC37 - 7537 - 75
312GGUU(chain G and (resid 1 through 33 or resid 37 through 75))GF1 - 331 - 33
322AACC(chain G and (resid 1 through 33 or resid 37 through 75))GF37 - 7537 - 75
412GGCCchain HHG1 - 751 - 75

NCS ensembles :
ID
1
2

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Components

#1: Protein
N-acetyltransferase domain-containing protein


Mass: 18816.625 Da / Num. of mol.: 4 / Mutation: Y140F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: STM3651 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ZL98
#2: RNA chain
RNA (76-MER)


Mass: 24478.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1609454293
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-AAC / ACETYLAMINO-ACETIC ACID


Mass: 117.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO3
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200mM calcium acetate, 100mM sodium cacodylate, pH 6.0, 14% (v/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.098→49.04 Å / Num. obs: 29107 / % possible obs: 99.3 % / Redundancy: 7.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.237 / Net I/σ(I): 7.6
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2823 / CC1/2: 0.606

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fvj

5fvj


Resolution: 3.098→49.04 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.98 / Stereochemistry target values: ML
Details: N-acetylglycine is covalently attached to 3'O of A76 in tRNA molecules to form aminoacyl-bond. The electron density for the aminoacyl moiety was observed only for chain E, thus it was not ...Details: N-acetylglycine is covalently attached to 3'O of A76 in tRNA molecules to form aminoacyl-bond. The electron density for the aminoacyl moiety was observed only for chain E, thus it was not modeled for the other tRNA molecules.
RfactorNum. reflection% reflection
Rfree0.2631 1455 5.01 %
Rwork0.2085 27614 -
obs0.2112 29069 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.18 Å2 / Biso mean: 72.7641 Å2 / Biso min: 21.93 Å2
Refinement stepCycle: final / Resolution: 3.098→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 6340 48 0 11302
Biso mean--84.76 --
Num. residues----931
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2973X-RAY DIFFRACTION11.627TORSIONAL
12B2973X-RAY DIFFRACTION11.627TORSIONAL
13C2973X-RAY DIFFRACTION11.627TORSIONAL
14D2973X-RAY DIFFRACTION11.627TORSIONAL
21E3432X-RAY DIFFRACTION11.627TORSIONAL
22F3432X-RAY DIFFRACTION11.627TORSIONAL
23G3432X-RAY DIFFRACTION11.627TORSIONAL
24H3432X-RAY DIFFRACTION11.627TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0983-3.2090.36631410.3115268098
3.209-3.33740.32671460.2603275299
3.3374-3.48930.28281450.2348275699
3.4893-3.67320.26791440.23752742100
3.6732-3.90320.2861460.22222764100
3.9032-4.20450.27651460.22773100
4.2045-4.62730.26621460.18132778100
4.6273-5.29620.2321480.17552807100
5.2962-6.670.23531460.20032779100
6.67-49.040.23561470.1949278398

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