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- PDB-6p8t: Acinetobacter baumannii tRNA synthetase in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 6p8t
TitleAcinetobacter baumannii 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 / cytoplasm
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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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
DepositionJun 7, 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 beta subunit
B: Phenylalanine--tRNA ligase beta subunit
C: Phenylalanine--tRNA ligase alpha subunit
D: Phenylalanine--tRNA ligase alpha subunit
E: Phenylalanine--tRNA ligase beta subunit
F: Phenylalanine--tRNA ligase beta subunit
G: Phenylalanine--tRNA ligase alpha subunit
H: Phenylalanine--tRNA ligase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,97815
Polymers500,0448
Non-polymers9347
Water543
1
A: Phenylalanine--tRNA ligase beta subunit
B: Phenylalanine--tRNA ligase beta subunit
C: Phenylalanine--tRNA ligase alpha subunit
D: Phenylalanine--tRNA ligase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,5018
Polymers250,0224
Non-polymers4794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23490 Å2
ΔGint-123 kcal/mol
Surface area88460 Å2
MethodPISA
2
E: Phenylalanine--tRNA ligase beta subunit
F: Phenylalanine--tRNA ligase beta subunit
G: Phenylalanine--tRNA ligase alpha subunit
H: Phenylalanine--tRNA ligase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,4777
Polymers250,0224
Non-polymers4553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23780 Å2
ΔGint-120 kcal/mol
Surface area80330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.266, 172.467, 191.891
Angle α, β, γ (deg.)90.000, 103.113, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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


Mass: 87791.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: pheT, HMPREF0010_01651 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0CA71, phenylalanine-tRNA ligase
#2: Protein
Phenylalanine--tRNA ligase alpha subunit / Phenylalanyl-tRNA synthetase alpha subunit / PheRS


Mass: 37219.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: pheS, HMPREF0010_01652 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0CA72, phenylalanine-tRNA ligase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NO4 / N-benzyl-2-(cyclohex-1-en-1-yl)ethan-1-amine


Mass: 215.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H21N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 17% PEG 8,000; 200 mM Mg(OAc)2; 100 mM NaCacodylate pH 6.2; 8 mM MgCl2; 8% 1,2,4-Butanetriol

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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: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.15→19.923 Å / Num. obs: 99384 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 95.74 Å2 / CC1/2: 0.993 / Net I/σ(I): 5.6
Reflection shellResolution: 3.15→3.2 Å / Num. unique obs: 4674 / CC1/2: 0.266 / % possible all: 92.4

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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: 3.15→19.92 Å / SU ML: 0.4755 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.6324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 1617 1.63 %
Rwork0.236 97529 -
obs0.2363 99146 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.62 Å2
Refinement stepCycle: LAST / Resolution: 3.15→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30153 0 67 3 30223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001430775
X-RAY DIFFRACTIONf_angle_d0.44141860
X-RAY DIFFRACTIONf_chiral_restr0.04024802
X-RAY DIFFRACTIONf_plane_restr0.00315553
X-RAY DIFFRACTIONf_dihedral_angle_d17.68211072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.240.37251380.33617991X-RAY DIFFRACTION97.6
3.24-3.350.36131400.33068104X-RAY DIFFRACTION98.52
3.35-3.470.35691340.30358113X-RAY DIFFRACTION98.92
3.47-3.60.35241340.29358111X-RAY DIFFRACTION98.65
3.6-3.770.29311350.28358107X-RAY DIFFRACTION98.75
3.77-3.960.2811240.25858123X-RAY DIFFRACTION98.65
3.96-4.210.29731380.22888181X-RAY DIFFRACTION98.66
4.21-4.530.241320.21138098X-RAY DIFFRACTION98.55
4.53-4.980.22541320.1968077X-RAY DIFFRACTION98.09
4.98-5.690.24171370.21728179X-RAY DIFFRACTION98.99
5.69-7.110.23451370.24598219X-RAY DIFFRACTION99.15
7.11-19.920.20421360.2028226X-RAY DIFFRACTION98.34

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