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- PDB-9drs: Crystal structure of M. tuberculosis PheRS-tRNA complex bound to ... -

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Basic information

Entry
Database: PDB / ID: 9drs
TitleCrystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-116
Components
  • (Phenylalanine--tRNA ligase ...) x 2
  • tRNA(Phe)
KeywordsLIGASE/RNA / RNA ligase aminoacyl-tRNA synthetase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / RNA BINDING PROTEIN / LIGASE-RNA complex
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 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanine-tRNA ligase, class IIc, beta subunit / 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
ACETATE ION / 1H-benzimidazol-2-amine / DI(HYDROXYETHYL)ETHER / : / RNA / RNA (> 10) / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGade, P. / Chang, C. / Forte, B. / Wower, J. / Gilbert, I.H. / Baragana, B. / Michalska, K. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Different chemical scaffolds bind to L-phe site in Mycobacterium tuberculosis Phe-tRNA synthetase.
Authors: Gade, P. / Chang, C. / Pryde, D.S. / Fletcher, D. / Niven, S. / Magalhaes, L.G. / Robinson, D. / Saini, J. / Ibrahim, P.E.G.F. / Forte, B. / Wower, J. / Bodkin, M.J. / Baragana, B. / ...Authors: Gade, P. / Chang, C. / Pryde, D.S. / Fletcher, D. / Niven, S. / Magalhaes, L.G. / Robinson, D. / Saini, J. / Ibrahim, P.E.G.F. / Forte, B. / Wower, J. / Bodkin, M.J. / Baragana, B. / Gilbert, I.H. / Michalska, K. / Joachimiak, A.
History
DepositionSep 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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: tRNA(Phe)
D: Phenylalanine--tRNA ligase alpha subunit
E: Phenylalanine--tRNA ligase beta subunit
F: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,86945
Polymers302,2516
Non-polymers2,61939
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40190 Å2
ΔGint-207 kcal/mol
Surface area108730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.676, 64.106, 188.334
Angle α, β, γ (deg.)90.00, 111.21, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Phenylalanine--tRNA ligase ... , 2 types, 4 molecules ADBE

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


Mass: 37415.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: pheS, Rv1649, MTCY06H11.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU3, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 88867.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: pheT, Rv1650, MTCY06H11.15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU1, phenylalanine-tRNA ligase

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RNA chain , 1 types, 2 molecules CF

#3: RNA chain tRNA(Phe)


Mass: 24842.811 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
References: GenBank: 1251771558

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Non-polymers , 8 types, 761 molecules

#4: Chemical ChemComp-AX7 / 1H-benzimidazol-2-amine


Mass: 133.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium Acetate, 0.1 M Hepes pH 7.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 135377 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.47 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 16.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6682 / CC1/2: 0.549 / CC star: 0.842 / Rpim(I) all: 0.486 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.77 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 10245 5.04 %
Rwork0.2006 --
obs0.2031 127062 76.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17318 3045 170 722 21255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221258
X-RAY DIFFRACTIONf_angle_d0.4529676
X-RAY DIFFRACTIONf_dihedral_angle_d9.3844258
X-RAY DIFFRACTIONf_chiral_restr0.0383510
X-RAY DIFFRACTIONf_plane_restr0.0043399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.38591060.32872176X-RAY DIFFRACTION26
2.38-2.410.3991410.31112609X-RAY DIFFRACTION32
2.41-2.440.31951720.30353152X-RAY DIFFRACTION38
2.44-2.470.32191880.29713701X-RAY DIFFRACTION43
2.47-2.50.32562450.28814056X-RAY DIFFRACTION49
2.5-2.540.31422150.27184368X-RAY DIFFRACTION52
2.54-2.570.31662660.26224709X-RAY DIFFRACTION56
2.57-2.610.2952540.24694783X-RAY DIFFRACTION58
2.61-2.650.28362830.25155039X-RAY DIFFRACTION59
2.65-2.70.28482680.25175317X-RAY DIFFRACTION64
2.7-2.740.28672680.2495681X-RAY DIFFRACTION68
2.74-2.790.29453370.25376009X-RAY DIFFRACTION71
2.79-2.850.29053360.24466365X-RAY DIFFRACTION76
2.85-2.90.31333350.24216675X-RAY DIFFRACTION79
2.9-2.970.29343960.23296867X-RAY DIFFRACTION83
2.97-3.040.29344350.22387181X-RAY DIFFRACTION86
3.04-3.110.25084030.21517455X-RAY DIFFRACTION90
3.11-3.20.2824770.20637766X-RAY DIFFRACTION92
3.2-3.290.25193930.20857608X-RAY DIFFRACTION92
3.29-3.40.25154250.20628302X-RAY DIFFRACTION98
3.4-3.520.23454390.20238241X-RAY DIFFRACTION99
3.52-3.660.25124400.18828321X-RAY DIFFRACTION99
3.66-3.820.20954430.17818360X-RAY DIFFRACTION99
3.82-4.030.22944650.17928336X-RAY DIFFRACTION99
4.03-4.280.21934360.17078238X-RAY DIFFRACTION98
4.28-4.610.22233720.16278402X-RAY DIFFRACTION99
4.61-5.070.21653960.16778386X-RAY DIFFRACTION100
5.07-5.80.22934570.18518367X-RAY DIFFRACTION100
5.8-7.310.23054310.19288248X-RAY DIFFRACTION99
7.31-46.770.22434230.17438306X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.1972 Å / Origin y: 0.0412 Å / Origin z: 45.0665 Å
111213212223313233
T0.1079 Å2-0.032 Å2-0.0073 Å2-0.0761 Å2-0.0167 Å2--0.1117 Å2
L0.0855 °2-0.0472 °2-0.1074 °2-0.0259 °20.0075 °2--0.2256 °2
S-0.013 Å °0.0723 Å °-0.0184 Å °0.0054 Å °0.0048 Å °0.0118 Å °0.0517 Å °-0.0403 Å °-0.0027 Å °
Refinement TLS groupSelection details: all

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