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

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Basic information

Entry
Database: PDB / ID: 9sfq
TitleStructure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type tRNATyr(GUC).
Components
  • Tyrosine--tRNA ligase
  • Wild-type, fully modified Thermus thermopilus tRNATyr(GUC)
KeywordsRNA BINDING PROTEIN / aminoacyl-tRNA synthetase / ligase / aminoacyl-adenylate
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
DI(HYDROXYETHYL)ETHER / RNA / RNA (> 10) / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 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: Tyrosine--tRNA ligase
T: Wild-type, fully modified Thermus thermopilus tRNATyr(GUC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,06021
Polymers76,7092
Non-polymers2,35119
Water10,287571
1
A: Tyrosine--tRNA ligase
T: Wild-type, fully modified Thermus thermopilus tRNATyr(GUC)
hetero molecules

A: Tyrosine--tRNA ligase
T: Wild-type, fully modified Thermus thermopilus tRNATyr(GUC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,12142
Polymers153,4184
Non-polymers4,70238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area30090 Å2
ΔGint-189 kcal/mol
Surface area58540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.319, 67.546, 111.169
Angle α, β, γ (deg.)90.000, 110.210, 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

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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 Wild-type, fully modified Thermus thermopilus tRNATyr(GUC)


Mass: 27922.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Wild-type fully modified tRNATyr(GUC). Modifications deduced from X-ray electron density map, not validated biochemically.
Source: (natural) Thermus thermophilus (bacteria)

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Non-polymers , 5 types, 590 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion / Details: Crystallised with PEG8000 Cryoprotectant PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97842 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97842 Å / Relative weight: 1
ReflectionResolution: 1.89→29.5 Å / Num. obs: 67751 / % possible obs: 98.3 % / Redundancy: 2.1 % / Biso Wilson estimate: 22.51 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 9
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.329 / Num. unique obs: 4334

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→29.5 Å / SU ML: 0.202 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 3424 5.06 %
Rwork0.1728 64298 -
obs0.1746 67722 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.89 Å2
Refinement stepCycle: LAST / Resolution: 1.89→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 1840 151 571 5947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895864
X-RAY DIFFRACTIONf_angle_d1.15518333
X-RAY DIFFRACTIONf_chiral_restr0.0528973
X-RAY DIFFRACTIONf_plane_restr0.0098740
X-RAY DIFFRACTIONf_dihedral_angle_d20.81082924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.920.3331000.28542110X-RAY DIFFRACTION76.79
1.92-1.950.29651390.24822665X-RAY DIFFRACTION98.98
1.95-1.980.27741490.22472692X-RAY DIFFRACTION99.23
1.98-2.010.24341590.20662691X-RAY DIFFRACTION99.16
2.01-2.050.24211430.20362683X-RAY DIFFRACTION99.3
2.05-2.080.25651530.20472683X-RAY DIFFRACTION99.02
2.08-2.120.23571430.20072687X-RAY DIFFRACTION99.33
2.12-2.170.24941390.19242703X-RAY DIFFRACTION99.3
2.17-2.210.23421420.18482702X-RAY DIFFRACTION99.13
2.21-2.270.22651440.18092697X-RAY DIFFRACTION99.54
2.27-2.320.24061520.17772718X-RAY DIFFRACTION99.55
2.32-2.390.21391590.17152680X-RAY DIFFRACTION99.4
2.39-2.460.21171340.17462715X-RAY DIFFRACTION99.65
2.46-2.530.20141440.16852719X-RAY DIFFRACTION99.62
2.53-2.620.22461320.1752721X-RAY DIFFRACTION99.41
2.63-2.730.23181330.18122723X-RAY DIFFRACTION99.3
2.73-2.850.21661640.18412688X-RAY DIFFRACTION99.55
2.85-30.23511590.17882695X-RAY DIFFRACTION99.55
3-3.190.18411410.17662739X-RAY DIFFRACTION99.45
3.19-3.440.21581400.17232705X-RAY DIFFRACTION99.09
3.44-3.780.17731460.1542719X-RAY DIFFRACTION98.86
3.78-4.330.1531350.13852724X-RAY DIFFRACTION98.48
4.33-5.450.15611450.13642723X-RAY DIFFRACTION98.02
5.45-29.50.21091290.1672716X-RAY DIFFRACTION95.47

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