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- PDB-9wqt: Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 9wqt
TitleCrystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with reveromycin A and isoleucine
ComponentsIsoleucine--tRNA ligase, cytoplasmic
KeywordsLIGASE / isoleucyl-tRNA synthetase / reveromycin
Function / homology
Function and homology information


isoleucine-tRNA ligase / isoleucyl-tRNA aminoacylation / isoleucine-tRNA ligase activity / aminoacyl-tRNA deacylase activity / sequence-specific mRNA binding / tRNA binding / ATP binding / cytosol
Similarity search - Function
Domain of unknown function (DUF5915) / Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding ...Domain of unknown function (DUF5915) / Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / 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-GVU / ISOLEUCINE / Isoleucine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, B. / Yi, F. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22207133 China
CitationJournal: Arch.Biochem.Biophys. / Year: 2026
Title: Substrate l-isoleucine facilitates the hyper inhibition of reveromycin A on human cytoplasmic isoleucyl-tRNA synthetase.
Authors: Chen, B. / Yi, F. / Qi, H. / Xu, J. / Su, J. / Zhou, H. / Liu, H.
History
DepositionSep 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoleucine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8436
Polymers113,8651
Non-polymers9785
Water10,953608
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.811, 65.042, 142.109
Angle α, β, γ (deg.)90.00, 107.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Isoleucine--tRNA ligase, cytoplasmic / Isoleucyl-tRNA synthetase / IleRS


Mass: 113864.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ILS1, YBL076C, YBL0734 / Production host: Escherichia coli (E. coli) / References: UniProt: P09436, isoleucine-tRNA ligase
#2: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GVU / (2E,4S,5S,6E,8E)-10-[(2S,3R,6S,8R,9S)-3-butyl-9-methyl-2-[(1E,3E)-3-methyl-5-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-3-(4-oxidanyl-4-oxidanylidene-butanoyl)oxy-1,7-dioxaspiro[5.5]undecan-8-yl]-4,8-dimethyl-5-oxidanyl-deca-2,6,8-trienoic acid


Mass: 660.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C36H52O11 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M BIS-Tris pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 116732 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.057 / Rrim(I) all: 0.105 / Χ2: 1.524 / Net I/σ(I): 6.9 / Num. measured all: 382625
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.973.20.448115940.8810.9680.2930.5370.54399.8
1.97-2.0530.362115270.8940.9720.2450.4380.68399.1
2.05-2.143.20.276115710.9310.9820.1790.330.84999.7
2.14-2.253.30.196116230.9710.9930.1250.2320.94299.8
2.25-2.393.30.16116670.9730.9930.1030.1911.2799.8
2.39-2.583.20.136115970.9760.9940.0890.1631.70199.6
2.58-2.843.40.111117040.9820.9950.070.1312.05799.8
2.84-3.253.30.094117140.9850.9960.0610.1122.19999.9
3.25-4.093.50.074117540.9890.9970.0460.0882.513100
4.09-503.30.069119810.9720.9930.0450.0832.186100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.407 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21949 5818 5 %RANDOM
Rwork0.19298 ---
obs0.19429 110905 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.478 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-1.81 Å2
2--3.88 Å20 Å2
3----2.07 Å2
Refinement stepCycle: 1 / Resolution: 1.9→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7425 0 68 608 8101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177139
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.64510528
X-RAY DIFFRACTIONr_angle_other_deg1.21.58716558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1275927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30922.698404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.184151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8551541
X-RAY DIFFRACTIONr_chiral_restr0.0570.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021679
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7193.4643705
X-RAY DIFFRACTIONr_mcbond_other1.7193.4643704
X-RAY DIFFRACTIONr_mcangle_it2.5485.1854633
X-RAY DIFFRACTIONr_mcangle_other2.5475.1844634
X-RAY DIFFRACTIONr_scbond_it1.9553.6314050
X-RAY DIFFRACTIONr_scbond_other1.9533.6314047
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1375.3465896
X-RAY DIFFRACTIONr_long_range_B_refined4.81440.2468963
X-RAY DIFFRACTIONr_long_range_B_other4.67139.8968812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 410 -
Rwork0.284 8045 -
obs--98.09 %

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