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- PDB-9kw0: Crystal structure of S. aureus tryptophanyl-tRNA synthetase compl... -

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Basic information

Entry
Database: PDB / ID: 9kw0
TitleCrystal structure of S. aureus tryptophanyl-tRNA synthetase complexed with tryptophan
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
TRYPTOPHAN / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsRen, Y. / Qiao, H. / 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)113,9786
Polymers113,3653
Non-polymers6133
Water4,071226
1
A: Tryptophan--tRNA ligase
hetero molecules

A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9854
Polymers75,5772
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4420 Å2
ΔGint-11 kcal/mol
Surface area26530 Å2
MethodPISA
2
B: Tryptophan--tRNA ligase
hetero molecules

C: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9854
Polymers75,5772
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area4160 Å2
ΔGint-17 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.684, 66.929, 98.602
Angle α, β, γ (deg.)90.000, 101.717, 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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
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: BL19U1 / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.32→62.85 Å / Num. obs: 51262 / % possible obs: 99.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 36.83 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 10.3
Reflection shellResolution: 2.32→2.45 Å / Rmerge(I) obs: 0.662 / Num. unique obs: 7474

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→62.85 Å / SU ML: 0.2233 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 1993 3.89 %
Rwork0.1981 49180 -
obs0.1988 51173 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.74 Å2
Refinement stepCycle: LAST / Resolution: 2.32→62.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7492 0 45 226 7763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00847670
X-RAY DIFFRACTIONf_angle_d1.01610352
X-RAY DIFFRACTIONf_chiral_restr0.05531158
X-RAY DIFFRACTIONf_plane_restr0.02021342
X-RAY DIFFRACTIONf_dihedral_angle_d6.13871032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.30151420.27283502X-RAY DIFFRACTION99.1
2.38-2.440.30771430.25863492X-RAY DIFFRACTION99.24
2.44-2.520.25981420.25963512X-RAY DIFFRACTION99.56
2.52-2.60.28121430.25343519X-RAY DIFFRACTION99.05
2.6-2.690.25691390.24093483X-RAY DIFFRACTION98.34
2.69-2.80.25751400.23823424X-RAY DIFFRACTION97.14
2.8-2.920.23381430.2333534X-RAY DIFFRACTION99.35
2.92-3.080.23671420.22873517X-RAY DIFFRACTION99.48
3.08-3.270.26611430.22433520X-RAY DIFFRACTION99.7
3.27-3.520.22431430.20563522X-RAY DIFFRACTION98.34
3.52-3.880.22691400.1913456X-RAY DIFFRACTION97.98
3.88-4.440.17711450.16363576X-RAY DIFFRACTION99.71
4.44-5.590.17141430.15973519X-RAY DIFFRACTION97.71
5.59-62.850.16171450.16013604X-RAY DIFFRACTION97.73

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