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- PDB-9ky9: Crystal structure of E. coli tryptophanyl-tRNA synthetase complex... -

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Basic information

Entry
Database: PDB / ID: 9ky9
TitleCrystal structure of E. coli tryptophanyl-tRNA synthetase complexed with 3-methylchuangxinmycin and tryptophanyl-5'-AMP
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / tryptophanyl-tRNA synthetase / aminoacyl-tRNA synthetase / antibiotic
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytosol
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / : / Tryptophan-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsRen, Y. / Wang, S. / Liu, W. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303100 China
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Mechanistic insights into the ATP-mediated and species-dependent inhibition of TrpRS by chuangxinmycin.
Authors: Ren, Y. / Wang, S. / Liu, W. / Wang, J. / Fang, P.
History
DepositionDec 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase
B: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6006
Polymers76,6272
Non-polymers9734
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-68 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.761, 90.851, 74.753
Angle α, β, γ (deg.)90.000, 109.472, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS


Mass: 38313.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_ ...Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_002885, C3F40_19370, CG704_07870, CIG67_21025, CTR35_001866, D9D43_04205, DD762_12005, DL968_00250, DNQ45_04190, DTL43_13995, DU321_12325, E4K51_10330, E6D34_04225, EIA08_11870, EPS97_04620, F7F11_12075, F7N46_14665, F9413_17445, F9461_03030, F9B07_12605, FGAF848_25410, FKO60_13960, FOI11_018845, FOI11_04335, FPS11_03390, FZU14_04195, G3V95_06005, G4A38_16925, G4A47_18515, G5603_11025, GAI89_06310, GNW61_08470, GOP25_12480, GP944_08250, GQE86_01825, GQN24_10725, HEP34_002452, HI055_002233, HJQ60_002846, HL563_11055, HL601_09110, HLX92_09755, HLZ50_06610, HMV95_07850, HVW04_17215, HVW43_18350, HVY77_01760, I6H00_19775, IH772_08800, J0541_002134, JNP96_25720, NCTC10764_03793, NCTC10974_00460, NCTC9044_01447, NCTC9073_00479, NCTC9077_00527, NCTC9706_02656, P6223_000209, Q2V20_09290, QDW62_01780, QO046_14075, R8G00_13645, SAMEA3472044_01080, SAMEA3472056_01981, SAMEA3752557_02035
Production host: Escherichia coli (E. coli) / References: UniProt: E2QFN4, tryptophan-tRNA ligase
#2: Chemical ChemComp-A1EHN / (6~{R})-5,5-dimethyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid / Meloxicam


Mass: 247.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate, 0.1 M MES, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.19→70.48 Å / Num. obs: 40144 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 28.55 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 8
Reflection shellResolution: 2.19→2.25 Å / Rmerge(I) obs: 0.489 / Num. unique obs: 2936

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8I1W
Resolution: 2.19→70.48 Å / SU ML: 0.2772 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 1993 5.03 %
Rwork0.2081 37667 -
obs0.2095 39660 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.74 Å2
Refinement stepCycle: LAST / Resolution: 2.19→70.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 64 236 5410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00835279
X-RAY DIFFRACTIONf_angle_d0.99377163
X-RAY DIFFRACTIONf_chiral_restr0.0528796
X-RAY DIFFRACTIONf_plane_restr0.008941
X-RAY DIFFRACTIONf_dihedral_angle_d5.8715761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.51341370.47842457X-RAY DIFFRACTION91.63
2.24-2.310.41491450.39982627X-RAY DIFFRACTION96.92
2.31-2.370.29061310.2442731X-RAY DIFFRACTION99.65
2.37-2.450.26171470.21882681X-RAY DIFFRACTION99.37
2.45-2.540.27021470.21622682X-RAY DIFFRACTION99.79
2.54-2.640.28621420.2192706X-RAY DIFFRACTION99.86
2.64-2.760.28941420.25042696X-RAY DIFFRACTION98.82
2.76-2.90.27871460.23312709X-RAY DIFFRACTION99.79
2.9-3.090.27711420.21812733X-RAY DIFFRACTION100
3.09-3.320.21241450.20662700X-RAY DIFFRACTION100
3.33-3.660.20171450.19842734X-RAY DIFFRACTION99.31
3.66-4.190.19871420.17942711X-RAY DIFFRACTION99.41
4.19-5.280.18571380.1482746X-RAY DIFFRACTION99.97
5.28-70.480.15961440.16042754X-RAY DIFFRACTION98.74

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