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

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Basic information

Entry
Database: PDB / ID: 9kxb
TitleCrystal structure of S. aureus tryptophanyl-tRNA synthetase complexed with 3-methylchuangxinmycin
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--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 6, 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)114,1076
Polymers113,3653
Non-polymers7423
Water5,080282
1
A: Tryptophan--tRNA ligase
hetero molecules

A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0714
Polymers75,5772
Non-polymers4952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5430 Å2
ΔGint-14 kcal/mol
Surface area28020 Å2
MethodPISA
2
B: Tryptophan--tRNA ligase
hetero molecules

C: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0714
Polymers75,5772
Non-polymers4952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area5370 Å2
ΔGint-19 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.946, 66.754, 100.169
Angle α, β, γ (deg.)90.000, 101.729, 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-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.: 3 / Source method: obtained synthetically / Formula: C13H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
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: 2.21→98.08 Å / Num. obs: 60230 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 36.09 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 6.5
Reflection shellResolution: 2.21→2.27 Å / Rmerge(I) obs: 0.81 / Num. unique obs: 4430

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→60.66 Å / SU ML: 0.2657 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2201 1996 3.32 %
Rwork0.2116 58038 -
obs0.2119 60034 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.96 Å2
Refinement stepCycle: LAST / Resolution: 2.21→60.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7517 0 51 282 7850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857704
X-RAY DIFFRACTIONf_angle_d1.039810407
X-RAY DIFFRACTIONf_chiral_restr0.0571161
X-RAY DIFFRACTIONf_plane_restr0.01171360
X-RAY DIFFRACTIONf_dihedral_angle_d6.33521080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.36981420.34814129X-RAY DIFFRACTION99.63
2.27-2.330.35321420.31534111X-RAY DIFFRACTION99.63
2.33-2.390.33441400.2794144X-RAY DIFFRACTION99.58
2.39-2.470.24721420.26274093X-RAY DIFFRACTION99.51
2.47-2.560.31321420.25634118X-RAY DIFFRACTION99.74
2.56-2.660.27191430.25234138X-RAY DIFFRACTION99.65
2.66-2.780.24981410.24824107X-RAY DIFFRACTION99.37
2.78-2.930.24091410.24494108X-RAY DIFFRACTION99.58
2.93-3.110.25571420.26414126X-RAY DIFFRACTION99.79
3.12-3.360.25521430.22844172X-RAY DIFFRACTION99.98
3.36-3.690.22861430.21414159X-RAY DIFFRACTION99.93
3.69-4.230.17341440.17544173X-RAY DIFFRACTION99.93
4.23-5.330.14881440.15684188X-RAY DIFFRACTION99.98
5.33-60.660.17411470.16224272X-RAY DIFFRACTION99.17

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