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- PDB-9kwh: Crystal structure of S. aureus tryptophanyl-tRNA synthetase compl... -

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Basic information

Entry
Database: PDB / ID: 9kwh
TitleCrystal structure of S. aureus tryptophanyl-tRNA synthetase complexed with chuangxinmycin
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 / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsRen, Y. / Qiao, H. / 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 5, 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
C: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0656
Polymers113,3653
Non-polymers7003
Water2,342130
1
A: Tryptophan--tRNA ligase
hetero molecules

A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0434
Polymers75,5772
Non-polymers4672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4400 Å2
ΔGint-13 kcal/mol
Surface area27350 Å2
MethodPISA
2
B: Tryptophan--tRNA ligase
hetero molecules

C: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0434
Polymers75,5772
Non-polymers4672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area4490 Å2
ΔGint-13 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.600, 66.520, 99.500
Angle α, β, γ (deg.)90.000, 101.650, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 37788.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: trpS, trpS_1, ACR74_03790, AS572_04105, BN1321_210001, C0102_00775, CNH36_04970, DQU50_00570, DQU51_12540, EIG96_10400, EP54_04615, EQ90_04625, G0Z31_13555, GO793_17575, GO814_04995, GO941_ ...Gene: trpS, trpS_1, ACR74_03790, AS572_04105, BN1321_210001, C0102_00775, CNH36_04970, DQU50_00570, DQU51_12540, EIG96_10400, EP54_04615, EQ90_04625, G0Z31_13555, GO793_17575, GO814_04995, GO941_08660, GO942_02330, GQX37_01775, GQX52_02140, GZ111_003340, HMPREF3211_01914, LB359_03465, M1K003_2422, NCTC10702_01521, NCTC13131_00650, SAMEA1029512_02646, SAMEA1029528_00434, SAMEA1029536_00113, SAMEA2078260_00480, SAMEA2078588_00140, SAMEA2080344_00170, SAMEA2081063_00170, SAMEA4008575_00170, SAMEA4552975_00916, SAMEA70146418_02923, SAMEA70153168_01652, SAMEA70245418_02512
Production host: Escherichia coli (E. coli) / References: UniProt: W8U075, 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.: 3 / Source method: isolated from a natural source / Formula: C12H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M Tris, 5% gamma-PGA (Na salt, low molecular), 20% PEG 2000 MME

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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: 2.38→30.23 Å / Num. obs: 47474 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 47.26 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.8
Reflection shellResolution: 2.38→2.44 Å / Rmerge(I) obs: 1.081 / Num. unique obs: 3454

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→30.23 Å / SU ML: 0.2747 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2028 1996 4.21 %
Rwork0.1953 45389 -
obs0.1957 47385 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.84 Å2
Refinement stepCycle: LAST / Resolution: 2.38→30.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7513 0 48 130 7691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857697
X-RAY DIFFRACTIONf_angle_d1.066710391
X-RAY DIFFRACTIONf_chiral_restr0.05611164
X-RAY DIFFRACTIONf_plane_restr0.02091357
X-RAY DIFFRACTIONf_dihedral_angle_d6.58841078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.33611400.32023196X-RAY DIFFRACTION99.43
2.44-2.510.34181410.29783191X-RAY DIFFRACTION99.14
2.51-2.580.31261420.2893224X-RAY DIFFRACTION99.38
2.58-2.660.28451430.26453260X-RAY DIFFRACTION99.44
2.66-2.760.24721410.253215X-RAY DIFFRACTION99.82
2.76-2.870.27511420.24623216X-RAY DIFFRACTION99.61
2.87-30.27741430.23453251X-RAY DIFFRACTION99.62
3-3.160.25391440.22353265X-RAY DIFFRACTION99.91
3.16-3.350.21571420.21353221X-RAY DIFFRACTION99.85
3.35-3.610.21091420.20493250X-RAY DIFFRACTION99.47
3.61-3.970.18131430.17823257X-RAY DIFFRACTION99.47
3.97-4.550.15771440.15723257X-RAY DIFFRACTION99.36
4.55-5.720.13881440.16623283X-RAY DIFFRACTION99.28
5.72-30.230.17191450.15113303X-RAY DIFFRACTION97.73

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