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- PDB-9sfb: Structure at 2.7 A resolution of Thermus thermophilus tyrosyl-tRN... -

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Basic information

Entry
Database: PDB / ID: 9sfb
TitleStructure at 2.7 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to a tRNA(Tyr)(GUA) transcript, the sulphamoyl analogue of tyrosyl-adenylate and pyrophosphate.
Components
  • Thermus thermophilus tRNATyr(GUC) transcript
  • 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
PYROPHOSPHATE / 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / RNA / RNA (> 10) / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 19, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
T: Thermus thermophilus tRNATyr(GUC) transcript
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,73210
Polymers76,4682
Non-polymers1,2648
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-96 kcal/mol
Surface area31360 Å2
Unit cell
Length a, b, c (Å)130.629, 130.629, 109.086
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#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 BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P83453, tyrosine-tRNA ligase
#2: RNA chain Thermus thermophilus tRNATyr(GUC) transcript


Mass: 27681.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: G9 replaced by U9 / Source: (synth.) Thermus thermophilus (bacteria)
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-YSA / 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / TYROSYLADENYLATE


Mass: 509.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O8S / Feature type: SUBJECT OF INVESTIGATION
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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: Don't know

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→23 Å / Num. obs: 29086 / % possible obs: 97.06 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.352 / Num. unique obs: 5814 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.36 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.5 / ESU R Free: 0.299
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2479 1449 4.982 %
Rwork0.2042 27637 -
all0.206 --
obs-29086 97.057 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 88.246 Å2
Baniso -1Baniso -2Baniso -3
1-1.459 Å20.73 Å2-0 Å2
2--1.459 Å2-0 Å2
3----4.734 Å2
Refinement stepCycle: LAST / Resolution: 2.7→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 1753 74 0 5220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125498
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174253
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.8647852
X-RAY DIFFRACTIONr_angle_other_deg0.3811.7499893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6095427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.484542
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.283567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66810632
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.16710161
X-RAY DIFFRACTIONr_chiral_restr0.0460.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021107
X-RAY DIFFRACTIONr_nbd_refined0.1910.21068
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.24027
X-RAY DIFFRACTIONr_nbtor_refined0.1960.22360
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.221
X-RAY DIFFRACTIONr_nbd_other0.1320.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.23
X-RAY DIFFRACTIONr_mcbond_it3.8028.2091708
X-RAY DIFFRACTIONr_mcbond_other3.7968.211708
X-RAY DIFFRACTIONr_mcangle_it5.77414.7662135
X-RAY DIFFRACTIONr_mcangle_other5.77414.7692136
X-RAY DIFFRACTIONr_scbond_it4.9079.5493790
X-RAY DIFFRACTIONr_scbond_other4.9069.5493791
X-RAY DIFFRACTIONr_scangle_it7.72517.3985717
X-RAY DIFFRACTIONr_scangle_other7.72417.3975718
X-RAY DIFFRACTIONr_lrange_it10.29298.1236461
X-RAY DIFFRACTIONr_lrange_other10.29198.1166462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7680.452750.3921537X-RAY DIFFRACTION74.9767
2.768-2.8430.398920.3591952X-RAY DIFFRACTION96.7803
2.843-2.9240.3641000.3121938X-RAY DIFFRACTION100
2.924-3.0120.3131200.2751869X-RAY DIFFRACTION100
3.012-3.1090.272790.2551877X-RAY DIFFRACTION100
3.109-3.2160.272890.2571783X-RAY DIFFRACTION100
3.216-3.3350.237990.2331712X-RAY DIFFRACTION100
3.335-3.4680.25910.2191625X-RAY DIFFRACTION100
3.468-3.6190.28770.2151623X-RAY DIFFRACTION100
3.619-3.7910.218750.2091534X-RAY DIFFRACTION99.9379
3.791-3.990.299890.1941436X-RAY DIFFRACTION100
3.99-4.2240.236720.1811395X-RAY DIFFRACTION100
4.224-4.5050.203730.1611299X-RAY DIFFRACTION100
4.505-4.850.189810.1591210X-RAY DIFFRACTION99.9226
4.85-5.290.229750.1571119X-RAY DIFFRACTION100
5.29-5.8750.189380.1841056X-RAY DIFFRACTION100
5.875-6.7120.276470.2923X-RAY DIFFRACTION99.6917
6.712-8.0510.186330.181813X-RAY DIFFRACTION98.8318
8.051-10.7460.228310.183599X-RAY DIFFRACTION91.1722
10.746-230.459130.292337X-RAY DIFFRACTION74.1525

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