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- PDB-6p24: Escherichia coli tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 6p24
TitleEscherichia coli tRNA synthetase
Components(Phenylalanine--tRNA ligase ...) x 2
KeywordsLIGASE / Inhibitor / Aminoacyl-tRNA synthetase / PheRS / Antibacterial
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / tRNA synthetase B5 domain / B5 domain profile. ...Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
HEXANE-1,6-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsKahne, D. / Baidin, V. / Owens, T.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19-AI109764-05-8340 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Simple Secondary Amines Inhibit Growth of Gram-Negative Bacteria through Highly Selective Binding to Phenylalanyl-tRNA Synthetase.
Authors: Baidin, V. / Owens, T.W. / Lazarus, M.B. / Kahne, D.
History
DepositionMay 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: 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: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: Phenylalanine--tRNA ligase alpha subunit
D: Phenylalanine--tRNA ligase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,45056
Polymers249,6024
Non-polymers3,84852
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35970 Å2
ΔGint-55 kcal/mol
Surface area84180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.269, 173.583, 251.472
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Phenylalanine--tRNA ligase ... , 2 types, 4 molecules ACBD

#1: Protein Phenylalanine--tRNA ligase alpha subunit / Phenylalanyl-tRNA synthetase alpha subunit / PheRS


Mass: 37318.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pheS, b1714, JW5277 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08312, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 87483.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pheT, b1713, JW1703 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07395, phenylalanine-tRNA ligase

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Non-polymers , 8 types, 579 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG 8,000, 200 mM MgCl2, 100 mM Tris-HCl pH8.5, 2% 1,6-hexanediol, 3% d-Galactose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.115→173.58 Å / Num. obs: 152649 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 50.86 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.7
Reflection shellResolution: 2.115→2.15 Å / Num. unique obs: 6642 / CC1/2: 0.126

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCO

3pco


Resolution: 2.12→82.04 Å / SU ML: 0.351 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265 1994 1.31 %
Rwork0.2294 150494 -
obs0.2299 152488 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.39 Å2
Refinement stepCycle: LAST / Resolution: 2.12→82.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16499 0 244 527 17270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001817004
X-RAY DIFFRACTIONf_angle_d0.457823013
X-RAY DIFFRACTIONf_chiral_restr0.04182620
X-RAY DIFFRACTIONf_plane_restr0.00293024
X-RAY DIFFRACTIONf_dihedral_angle_d21.07066284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.3811250.34429817X-RAY DIFFRACTION92
2.17-2.230.36221410.330110590X-RAY DIFFRACTION99.11
2.23-2.290.34961430.311510722X-RAY DIFFRACTION99.67
2.29-2.370.331420.296910726X-RAY DIFFRACTION99.72
2.37-2.450.33921430.29410701X-RAY DIFFRACTION99.25
2.45-2.550.31461410.288210706X-RAY DIFFRACTION99.52
2.55-2.670.34371440.280210752X-RAY DIFFRACTION99.8
2.67-2.810.32061430.270410752X-RAY DIFFRACTION99.82
2.81-2.980.31611420.241310752X-RAY DIFFRACTION99.89
2.98-3.210.26351450.235410895X-RAY DIFFRACTION99.95
3.21-3.540.24161440.228510831X-RAY DIFFRACTION99.91
3.54-4.050.26461440.211310913X-RAY DIFFRACTION99.61
4.05-5.10.22711470.192111024X-RAY DIFFRACTION99.81
5.1-82.040.22421500.203611313X-RAY DIFFRACTION99.2

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