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- PDB-6p26: Escherichia coli tRNA synthetase in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 6p26
TitleEscherichia coli tRNA synthetase in complex with compound 1
Components
  • Phenylalanine--tRNA ligase alpha subunit
  • Phenylalanine--tRNA ligase beta subunit
KeywordsLIGASE / Inhibitor / Aminoacyl-tRNA synthetase / PheRS / Antibacterial
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / 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 / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain ...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 / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / B3/4 domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / 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
N-benzyl-2-(cyclohex-1-en-1-yl)ethan-1-amine / : / : / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 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 21, 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

Downloads & links

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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)250,0336
Polymers249,6024
Non-polymers4312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24370 Å2
ΔGint-79 kcal/mol
Surface area86080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.193, 174.040, 252.348
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

#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 str. K-12 substr. MG1655 (bacteria)
Gene: pheS, D8B36_10295 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A387D3L6, UniProt: P08312*PLUS, 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 str. K-12 substr. MG1655 (bacteria)
Gene: pheT, D8B36_10300 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A387D0Y5, UniProt: P07395*PLUS, phenylalanine-tRNA ligase
#3: Chemical ChemComp-NO4 / N-benzyl-2-(cyclohex-1-en-1-yl)ethan-1-amine


Mass: 215.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H21N / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 54.19 %
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, 3% 1,6-hexanediol, 2% 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: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.16→82.27 Å / Num. obs: 47360 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 68.61 Å2 / CC1/2: 0.979 / Net I/σ(I): 6.1
Reflection shellResolution: 3.16→3.27 Å / Num. unique obs: 4527 / CC1/2: 0.366

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCO

3pco


Resolution: 3.16→82.27 Å / SU ML: 0.4406 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 2000 4.25 %
Rwork0.2034 45090 -
obs0.2056 47090 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.42 Å2
Refinement stepCycle: LAST / Resolution: 3.16→82.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16564 0 32 0 16596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001416911
X-RAY DIFFRACTIONf_angle_d0.445322965
X-RAY DIFFRACTIONf_chiral_restr0.04192617
X-RAY DIFFRACTIONf_plane_restr0.00293039
X-RAY DIFFRACTIONf_dihedral_angle_d20.95566253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.240.34171410.29853175X-RAY DIFFRACTION99.43
3.24-3.330.35071400.27583147X-RAY DIFFRACTION99.64
3.33-3.420.33981410.27323192X-RAY DIFFRACTION99.61
3.42-3.530.32961400.25493159X-RAY DIFFRACTION99.7
3.54-3.660.31471420.22863173X-RAY DIFFRACTION99.43
3.66-3.810.22651420.21523208X-RAY DIFFRACTION99.79
3.81-3.980.28111400.20133163X-RAY DIFFRACTION99.67
3.98-4.190.29151420.19273212X-RAY DIFFRACTION99.67
4.19-4.450.25711430.19113220X-RAY DIFFRACTION99.73
4.45-4.80.23561420.16493201X-RAY DIFFRACTION99.49
4.8-5.280.20971420.16873220X-RAY DIFFRACTION98.91
5.28-6.040.23031460.18783270X-RAY DIFFRACTION99.85
6.04-7.610.25211460.20343316X-RAY DIFFRACTION99.83
7.61-82.270.19961530.18233434X-RAY DIFFRACTION98.84

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