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- PDB-6oz5: Escherichia coli tRNA synthetase in complex with compound 3 -

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Basic information

Entry
Database: PDB / ID: 6oz5
TitleEscherichia coli tRNA synthetase in complex with compound 3
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 / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-VB3 / : / : / 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: 2.5 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 15, 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)250,89918
Polymers249,6024
Non-polymers1,29614
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26930 Å2
ΔGint-57 kcal/mol
Surface area85630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.775, 174.508, 252.548
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 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

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Non-polymers , 6 types, 315 molecules

#3: Chemical ChemComp-VB3 / 2-({[(2S)-1-cyclohexylpropan-2-yl]amino}methyl)phenol


Mass: 247.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 8,000, 200 mM MgCl2, 100 mM Tris-HCl pH 8.5, 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: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→59.37 Å / Num. obs: 95661 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4659 / CC1/2: 0.516 / % possible all: 99.9

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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: 2.5→58.23 Å / SU ML: 0.359 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 2000 2.09 %
Rwork0.2065 93547 -
obs0.2073 95547 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16544 0 87 301 16932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002216934
X-RAY DIFFRACTIONf_angle_d0.51522980
X-RAY DIFFRACTIONf_chiral_restr0.04312625
X-RAY DIFFRACTIONf_plane_restr0.00313033
X-RAY DIFFRACTIONf_dihedral_angle_d20.44946251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.35911410.2986599X-RAY DIFFRACTION99.91
2.56-2.630.31871400.27566540X-RAY DIFFRACTION99.97
2.63-2.710.33441410.26486620X-RAY DIFFRACTION100
2.71-2.80.2881420.24286612X-RAY DIFFRACTION99.99
2.8-2.90.27741410.23386614X-RAY DIFFRACTION99.96
2.9-3.010.2821420.22086608X-RAY DIFFRACTION99.99
3.01-3.150.24921410.21776621X-RAY DIFFRACTION100
3.15-3.320.26481420.21746631X-RAY DIFFRACTION99.99
3.32-3.520.30861420.22336659X-RAY DIFFRACTION99.99
3.52-3.80.23491430.20656692X-RAY DIFFRACTION99.99
3.8-4.180.23161440.19516716X-RAY DIFFRACTION99.96
4.18-4.780.21231430.17286741X-RAY DIFFRACTION99.96
4.78-6.020.21781460.19356803X-RAY DIFFRACTION99.97
6.02-58.230.20891520.19147091X-RAY DIFFRACTION99.82

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