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- PDB-9sdf: Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRN... -

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Basic information

Entry
Database: PDB / ID: 9sdf
TitleStructure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type modified tRNA(Tyr), tyrosine and AMP
Components
  • Thermus thermophilus tRNA(Tyr)(GUA) (86-MER)
  • Tyrosine--tRNA ligase
KeywordsRNA BINDING PROTEIN / aminoacyl-tRNA synthetase / ligase / tRNA
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytosol
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 2 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / TYROSINE / RNA / RNA (> 10) / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCusack, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: EMBO J / Year: 2002
Title: Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition.
Authors: Yaremchuk, A. / Kriklivyi, I. / Tukalo, M. / Cusack, S.
History
DepositionAug 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
T: Thermus thermophilus tRNA(Tyr)(GUA) (86-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,32718
Polymers76,7102
Non-polymers2,61716
Water8,953497
1
A: Tyrosine--tRNA ligase
T: Thermus thermophilus tRNA(Tyr)(GUA) (86-MER)
hetero molecules

A: Tyrosine--tRNA ligase
T: Thermus thermophilus tRNA(Tyr)(GUA) (86-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,65436
Polymers153,4204
Non-polymers5,23432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area27020 Å2
ΔGint-173 kcal/mol
Surface area58020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.067, 67.378, 113.817
Angle α, β, γ (deg.)90.00, 112.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain , 2 types, 2 molecules AT

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 48786.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: tyrS, TT_C1033 / Production host: Escherichia coli (E. coli) / References: UniProt: P83453, tyrosine-tRNA ligase
#2: RNA chain Thermus thermophilus tRNA(Tyr)(GUA) (86-MER)


Mass: 27923.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria)

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Non-polymers , 8 types, 513 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: do not know Cryo: 22% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Aug 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→22.44 Å / Num. obs: 127578 / % possible obs: 99.1 % / Redundancy: 2.48 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.18
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.518 / Num. unique obs: 5005 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→16.74 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2139 5184 4.07 %
Rwork0.188 --
obs0.189 127458 94.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→16.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 1813 166 497 5883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045815
X-RAY DIFFRACTIONf_angle_d0.8958258
X-RAY DIFFRACTIONf_dihedral_angle_d21.422860
X-RAY DIFFRACTIONf_chiral_restr0.043964
X-RAY DIFFRACTIONf_plane_restr0.007744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.27641840.2654048X-RAY DIFFRACTION92
1.92-1.940.24471760.25713918X-RAY DIFFRACTION93
1.94-1.970.2511880.24464087X-RAY DIFFRACTION92
1.97-1.990.28121640.24053978X-RAY DIFFRACTION93
1.99-2.020.23191690.23564098X-RAY DIFFRACTION94
2.02-2.050.26861520.23164097X-RAY DIFFRACTION94
2.05-2.080.27891820.22614008X-RAY DIFFRACTION94
2.08-2.110.25011560.22094093X-RAY DIFFRACTION94
2.11-2.140.26781890.21724073X-RAY DIFFRACTION94
2.14-2.170.20261820.20424053X-RAY DIFFRACTION95
2.17-2.210.25891730.20994118X-RAY DIFFRACTION94
2.21-2.250.22291840.19884059X-RAY DIFFRACTION95
2.25-2.30.19811760.19564149X-RAY DIFFRACTION94
2.3-2.340.20071610.18674064X-RAY DIFFRACTION95
2.34-2.390.25242100.18644066X-RAY DIFFRACTION95
2.39-2.450.21241790.18774168X-RAY DIFFRACTION95
2.45-2.510.20691720.18844020X-RAY DIFFRACTION95
2.51-2.580.24332090.18864124X-RAY DIFFRACTION95
2.58-2.650.23851730.19054092X-RAY DIFFRACTION95
2.65-2.740.25731730.19944148X-RAY DIFFRACTION95
2.74-2.830.21251760.19974138X-RAY DIFFRACTION95
2.84-2.950.26531480.19544124X-RAY DIFFRACTION95
2.95-3.080.22181990.19624077X-RAY DIFFRACTION95
3.08-3.240.23921430.18664130X-RAY DIFFRACTION95
3.24-3.440.19021790.17754038X-RAY DIFFRACTION94
3.44-3.710.20011500.16534133X-RAY DIFFRACTION94
3.71-4.080.20791550.16034071X-RAY DIFFRACTION94
4.08-4.650.15871790.14434071X-RAY DIFFRACTION94
4.65-5.820.12541450.15714104X-RAY DIFFRACTION94
5.82-16.740.20991580.19513927X-RAY DIFFRACTION90

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