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

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Basic information

Entry
Database: PDB / ID: 9drv
TitleCrystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-004
Components
  • (Phenylalanine--tRNA ligase ...) x 2
  • tRNA(phe)
KeywordsLIGASE / RNA ligase aminoacyl-tRNAsynthetase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
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
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
QUINOLIN-2-AMINE / ACETATE ION / DI(HYDROXYETHYL)ETHER / : / RNA / RNA (> 10) / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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)306,70233
Polymers304,3856
Non-polymers2,31727
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38800 Å2
ΔGint-186 kcal/mol
Surface area109630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.091, 64.393, 188.776
Angle α, β, γ (deg.)90.00, 111.10, 90.00
Int Tables number4
Space group name H-MP1211

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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: 38482.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / 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)
Strain: ATCC 25618 / H37Rv / 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 (strain ATCC 25618 / H37Rv) (bacteria)
References: GenBank: 1251771558

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Non-polymers , 9 types, 775 molecules

#4: Chemical ChemComp-2AQ / QUINOLIN-2-AMINE / 2-AMINOQUINOLINE


Mass: 144.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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
Details: 0.1 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: Aug 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 119855 / % possible obs: 99.2 % / Redundancy: 4.2 % / CC1/2: 0.974 / CC star: 0.993 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.067 / Rrim(I) all: 0.144 / Χ2: 0.882 / Net I/σ(I): 6 / Num. measured all: 498751
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.45-2.493.91.21159660.5220.8280.6771.3930.86999.3
2.49-2.5441.02159260.650.8880.5561.1670.85999.1
2.54-2.594.10.9159450.7030.9090.4921.0390.89199
2.59-2.643.90.72358600.7480.9250.4010.830.87998.6
2.64-2.740.67259280.7940.9410.3650.7680.86998.8
2.7-2.764.40.57859780.8630.9630.3010.6540.88999.5
2.76-2.834.40.46959590.8980.9730.2450.5310.88899.6
2.83-2.94.30.3760090.9330.9820.1940.4190.90699.5
2.9-2.994.30.31359570.9420.9850.1650.3550.90499.4
2.99-3.094.20.25359690.9550.9880.1350.2880.91199.5
3.09-3.24.10.19960090.9590.990.1070.2270.93299.3
3.2-3.323.90.16658800.9720.9930.0910.190.92898.5
3.32-3.484.40.13960150.980.9950.0710.1560.90499.7
3.48-3.664.30.11860000.980.9950.0620.1340.90899.6
3.66-3.894.30.10360230.9780.9940.0540.1160.88899.6
3.89-4.194.10.0960190.9820.9950.0480.1030.88999.1
4.19-4.614.20.07960380.9840.9960.0420.090.78699.2
4.61-5.284.40.07360440.9890.9970.0380.0820.70699.5
5.28-6.6540.06160610.990.9970.0320.0690.57398.6
6.65-504.20.05762690.9830.9960.0310.0651.24599.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→48.75 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 7021 4.91 %
Rwork0.2099 --
obs0.2123 108242 60.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17452 3045 152 748 21397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221372
X-RAY DIFFRACTIONf_angle_d0.43729857
X-RAY DIFFRACTIONf_dihedral_angle_d8.9824295
X-RAY DIFFRACTIONf_chiral_restr0.0373529
X-RAY DIFFRACTIONf_plane_restr0.0043423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.490.4162720.36771450X-RAY DIFFRACTION19
2.49-2.510.45221020.3321697X-RAY DIFFRACTION23
2.52-2.550.34851080.32132002X-RAY DIFFRACTION27
2.55-2.580.33051000.32272318X-RAY DIFFRACTION30
2.58-2.610.33021140.30192576X-RAY DIFFRACTION35
2.61-2.650.38291310.29982853X-RAY DIFFRACTION38
2.65-2.690.32231670.29743156X-RAY DIFFRACTION42
2.69-2.730.34761500.29723443X-RAY DIFFRACTION46
2.73-2.770.29851720.28853585X-RAY DIFFRACTION48
2.77-2.810.34321860.28993739X-RAY DIFFRACTION50
2.81-2.860.30341830.28853739X-RAY DIFFRACTION50
2.86-2.910.29761910.28843879X-RAY DIFFRACTION51
2.91-2.970.33231860.28853903X-RAY DIFFRACTION52
2.97-3.030.32242010.28753938X-RAY DIFFRACTION53
3.03-3.10.3032100.27113987X-RAY DIFFRACTION54
3.1-3.170.33822300.25544077X-RAY DIFFRACTION55
3.17-3.250.30562390.24774156X-RAY DIFFRACTION56
3.25-3.340.27272510.24164325X-RAY DIFFRACTION59
3.34-3.430.31332620.22784899X-RAY DIFFRACTION66
3.43-3.540.28022730.2215255X-RAY DIFFRACTION71
3.54-3.670.28682680.2125773X-RAY DIFFRACTION77
3.67-3.820.23812890.19776172X-RAY DIFFRACTION82
3.82-3.990.273100.18766527X-RAY DIFFRACTION87
3.99-4.20.23563710.18126432X-RAY DIFFRACTION87
4.2-4.470.21123580.17496609X-RAY DIFFRACTION89
4.47-4.810.22553370.16636942X-RAY DIFFRACTION93
4.81-5.290.2334830.1727104X-RAY DIFFRACTION96
5.29-6.060.24054200.18277144X-RAY DIFFRACTION96
6.06-7.630.25333150.19247218X-RAY DIFFRACTION96
7.63-48.750.19123420.17986939X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 9.9305 Å / Origin y: -0.0504 Å / Origin z: 45.2385 Å
111213212223313233
T0.1197 Å2-0.014 Å2-0.0068 Å2-0.0858 Å2-0.0264 Å2--0.1216 Å2
L0.0658 °2-0.0315 °2-0.1045 °2-0.0554 °20.0094 °2--0.2119 °2
S-0.0141 Å °0.0508 Å °0.0015 Å °0.0203 Å °0.0048 Å °0.0063 Å °0.0356 Å °-0.0306 Å °-0.0067 Å °
Refinement TLS groupSelection details: all

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