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- PDB-7db8: Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA... -

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Basic information

Entry
Database: PDB / ID: 7db8
TitleCrystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase in complex with compound PF-3845
Components
  • Phenylalanine--tRNA ligase alpha subunit
  • Phenylalanine--tRNA ligase beta subunit
KeywordsLIGASE / aminoacylation / tRNA-binding / aminoacyl-tRNA synthetase / ATP-binding
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / peptidoglycan-based cell wall / tRNA binding / magnesium ion binding / ATP binding / plasma membrane / 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 / 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 / Phenylalanine-tRNA ligase, class IIc, beta subunit / 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
Chem-H2R / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, M. / Zhang, X. / Xu, L. / Chen, S.
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis .
Authors: Wang, H. / Xu, M. / Engelhart, C.A. / Zhang, X. / Yan, B. / Pan, M. / Xu, Y. / Fan, S. / Liu, R. / Xu, L. / Hua, L. / Schnappinger, D. / Chen, S.
#1: Journal: J.Biol.Chem. / Year: 2021
Title: Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis
Authors: Wang, H. / Xu, M. / Engelhart, C.A. / Zhang, X. / Yan, B. / Pan, M. / Xu, Y. / Fan, S. / Liu, R. / Xu, L. / Hua, L. / Schnappinger, D. / Chen, S.
History
DepositionOct 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,30016
Polymers127,5952
Non-polymers1,70514
Water18,4831026
1
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules

A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,60132
Polymers255,1904
Non-polymers3,41128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area25050 Å2
ΔGint-169 kcal/mol
Surface area86250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)278.005, 297.814, 65.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 37415.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pheS, Rv1649, MTCY06H11.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WFU3, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 90179.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pheT, Rv1650, MTCY06H11.15 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WFU1, phenylalanine-tRNA ligase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-H2R / N-pyridin-3-yl-4-[[3-[5-(trifluoromethyl)pyridin-2-yl]oxyphenyl]methyl]piperidine-1-carboxamide


Mass: 456.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23F3N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1026 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.5M (NH4)2SO4, 0.2% PEG 3350, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 121928 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 29.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.138 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 6050 / CC1/2: 0.953 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874phasing
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DAW

7daw


Resolution: 2.3→49.64 Å / SU ML: 0.1896 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1864 5476 4.89 %
Rwork0.1682 106404 -
obs0.1691 111880 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8341 0 98 1026 9465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818669
X-RAY DIFFRACTIONf_angle_d0.979611861
X-RAY DIFFRACTIONf_chiral_restr0.05961336
X-RAY DIFFRACTIONf_plane_restr0.00641594
X-RAY DIFFRACTIONf_dihedral_angle_d22.86143186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.24311430.20012617X-RAY DIFFRACTION68.25
2.33-2.350.20381200.19362712X-RAY DIFFRACTION69.6
2.35-2.380.26191360.1892684X-RAY DIFFRACTION71.14
2.38-2.410.21321260.1952814X-RAY DIFFRACTION73.56
2.41-2.440.21490.22928X-RAY DIFFRACTION75.69
2.44-2.480.23521280.19232929X-RAY DIFFRACTION77.29
2.48-2.510.22951350.20083063X-RAY DIFFRACTION78.81
2.51-2.550.22911280.20333156X-RAY DIFFRACTION81.15
2.55-2.590.24761600.23174X-RAY DIFFRACTION83.98
2.59-2.630.21831590.20793453X-RAY DIFFRACTION88.53
2.63-2.680.26522140.21643443X-RAY DIFFRACTION91.52
2.68-2.730.23112020.20773664X-RAY DIFFRACTION95.36
2.73-2.780.24011920.19923738X-RAY DIFFRACTION97.96
2.78-2.840.19912130.18913780X-RAY DIFFRACTION98.84
2.84-2.90.20631920.19623831X-RAY DIFFRACTION99.6
2.9-2.970.21641820.19013852X-RAY DIFFRACTION99.93
2.97-3.040.22092130.18643825X-RAY DIFFRACTION100
3.04-3.120.22272310.18553825X-RAY DIFFRACTION99.98
3.12-3.210.19571980.18683820X-RAY DIFFRACTION100
3.21-3.320.22391910.17613905X-RAY DIFFRACTION99.98
3.32-3.440.23491830.17163858X-RAY DIFFRACTION100
3.44-3.570.16272090.16193850X-RAY DIFFRACTION99.98
3.57-3.740.15781910.14813886X-RAY DIFFRACTION99.98
3.74-3.930.14632200.14393854X-RAY DIFFRACTION99.98
3.93-4.180.14772010.13573906X-RAY DIFFRACTION100
4.18-4.50.14512250.12643853X-RAY DIFFRACTION99.98
4.5-4.950.1422450.12833890X-RAY DIFFRACTION100
4.95-5.670.16951690.15253967X-RAY DIFFRACTION100
5.67-7.140.16812250.17113973X-RAY DIFFRACTION99.98
7.14-49.640.17081960.16624154X-RAY DIFFRACTION99.61

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