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

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Basic information

Entry
Database: PDB / ID: 7daw
TitleCrystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase
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 / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / peptidoglycan-based cell wall / tRNA binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Ferrodoxin-fold anticodon-binding 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 ...Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Ferrodoxin-fold anticodon-binding 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 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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 proteins / 3-Layer(bba) Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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 18, 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)128,74814
Polymers127,5952
Non-polymers1,15312
Water00
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)257,49628
Polymers255,1904
Non-polymers2,30624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area29760 Å2
ΔGint-480 kcal/mol
Surface area85400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)267.000, 298.910, 65.936
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.: 12 / Source method: obtained synthetically / Formula: SO4
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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.1M (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: 0.97886 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.83→50 Å / Num. obs: 59426 / % possible obs: 93.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 59.32 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.174 / Net I/σ(I): 10.86
Reflection shellResolution: 2.83→2.87 Å / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2275 / CC1/2: 0.84 / % possible all: 71.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874phasing
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCO

3pco


Resolution: 2.83→49.82 Å / SU ML: 0.3437 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 2984 5.03 %
Rwork0.1999 56362 -
obs0.2019 59346 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.02 Å2
Refinement stepCycle: LAST / Resolution: 2.83→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 60 0 8396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918625
X-RAY DIFFRACTIONf_angle_d1.103211799
X-RAY DIFFRACTIONf_chiral_restr0.06261335
X-RAY DIFFRACTIONf_plane_restr0.00771569
X-RAY DIFFRACTIONf_dihedral_angle_d23.30673152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.880.31791130.26991948X-RAY DIFFRACTION68.4
2.88-2.920.28381210.28532121X-RAY DIFFRACTION74.98
2.92-2.980.31441320.28062262X-RAY DIFFRACTION80.17
2.98-3.040.3181400.27922372X-RAY DIFFRACTION83.68
3.04-3.10.37461140.28442451X-RAY DIFFRACTION86.13
3.1-3.160.30111300.27932534X-RAY DIFFRACTION88.53
3.16-3.240.31751360.29672614X-RAY DIFFRACTION91.21
3.24-3.320.34961360.27532660X-RAY DIFFRACTION93.92
3.32-3.410.28851440.25082732X-RAY DIFFRACTION95.71
3.41-3.510.27051250.23412828X-RAY DIFFRACTION97.65
3.51-3.620.23091460.21462842X-RAY DIFFRACTION99.47
3.62-3.750.2291440.20422854X-RAY DIFFRACTION99.37
3.75-3.90.20571630.18932862X-RAY DIFFRACTION99.47
3.9-4.080.2411520.17362858X-RAY DIFFRACTION99.7
4.08-4.290.2241580.17212852X-RAY DIFFRACTION99.7
4.29-4.560.19391500.16112870X-RAY DIFFRACTION99.64
4.56-4.920.21861300.15382925X-RAY DIFFRACTION99.9
4.92-5.410.20851620.16892908X-RAY DIFFRACTION99.77
5.41-6.190.22781430.18472915X-RAY DIFFRACTION99.51
6.19-7.80.20921860.18072912X-RAY DIFFRACTION99.36
7.8-49.820.21111590.17593042X-RAY DIFFRACTION97.5

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