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

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Basic information

Entry
Database: PDB / ID: 9kxr
TitleCrystal structure of E. coli tryptophanyl-tRNA synthetase complexed with chuangxinmycin 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
Chem-9E0 / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 7, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,5866
Polymers76,6272
Non-polymers9594
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-68 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.078, 91.036, 75.106
Angle α, β, γ (deg.)90.000, 109.312, 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-9E0 / (5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid


Mass: 233.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO2S / 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.: 214 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5 / 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: 2.24→36 Å / Num. obs: 38054 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 5.5
Reflection shellResolution: 2.24→2.3 Å / Rmerge(I) obs: 0.813 / Num. unique obs: 2847

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8I1W

8i1w


Resolution: 2.24→35.44 Å / SU ML: 0.297 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 1999 5.27 %
Rwork0.2046 35902 -
obs0.2053 37901 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.92 Å2
Refinement stepCycle: LAST / Resolution: 2.24→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 63 214 5439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915332
X-RAY DIFFRACTIONf_angle_d1.02417235
X-RAY DIFFRACTIONf_chiral_restr0.0559801
X-RAY DIFFRACTIONf_plane_restr0.0184945
X-RAY DIFFRACTIONf_dihedral_angle_d8.8553745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.290.35551450.34052502X-RAY DIFFRACTION96.18
2.29-2.360.28431450.28482525X-RAY DIFFRACTION99.66
2.36-2.430.28731400.25062546X-RAY DIFFRACTION99.33
2.43-2.50.27371330.25382579X-RAY DIFFRACTION99.63
2.5-2.590.28041310.24792573X-RAY DIFFRACTION99.63
2.59-2.70.26751610.24412538X-RAY DIFFRACTION99.67
2.7-2.820.25441270.23612578X-RAY DIFFRACTION99.59
2.82-2.970.30891540.24652558X-RAY DIFFRACTION99.71
2.97-3.150.24351390.22972540X-RAY DIFFRACTION99.74
3.15-3.40.21981510.2172566X-RAY DIFFRACTION99.82
3.4-3.740.23131410.20052573X-RAY DIFFRACTION99.78
3.74-4.280.16731450.16512587X-RAY DIFFRACTION99.89
4.28-5.390.14231450.15292602X-RAY DIFFRACTION99.96
5.39-35.440.18121420.16722635X-RAY DIFFRACTION99.71

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