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- PDB-9slz: Structure of Thermus thermophilus lysyl-tRNA synthetase complexed... -

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Basic information

Entry
Database: PDB / ID: 9slz
TitleStructure of Thermus thermophilus lysyl-tRNA synthetase complexed with wild-type E.coli tRNALys(mnm5s2UUU) and sulphamoyl-analogue of lysyl-adenylate
Components
  • Lysine--tRNA ligase
  • Wild-type E. coli tRNALys
KeywordsRNA BINDING PROTEIN / amino-acyl-tRNA synthetase / tRNA / aminoacyl-adenylate
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / RNA / RNA (> 10) / Lysine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsCusack, S. / Yaremchuk, A. / Tukalo, M.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
Citation
Journal: EMBO J / Year: 1996
Title: The crystal structures of T. thermophilus lysyl-tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes ...Title: The crystal structures of T. thermophilus lysyl-tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue.
Authors: Cusack, S. / Yaremchuk, A. / Tukalo, M.
#1: Journal: Proteins / Year: 1995
Title: Cocrystallization of lysyl-tRNA synthetase from Thermus thermophilus with its cognate tRNAlys and with Escherichia coli tRNAlys.
Authors: Yaremchuk, A.D. / Krikliviy, I.A. / Cusack, S. / Tukalo, M.A.
History
DepositionSep 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 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: Lysine--tRNA ligase
T: Wild-type E. coli tRNALys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,13710
Polymers81,9902
Non-polymers1,1478
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-78 kcal/mol
Surface area26170 Å2
Unit cell
Length a, b, c (Å)147.300, 147.300, 127.450
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-501-

SO4

21A-505-

SO4

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Components

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 57003.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: lysS, TTHA1041 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJG7, lysine-tRNA ligase
#2: RNA chain Wild-type E. coli tRNALys


Mass: 24987.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N8O7S / 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: 4.87 Å3/Da / Density % sol: 74.73 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 24-26% saturated ammonium sulphate. 50 mM Tris-maleate (pH 7.6), 10 mM MgCI2, 1 mM NaN3, 4 mg/ml LysRSTT, 2.5 mg/ml wt Ecoli tRNALys and 325 microM LysAMS. Cryoprotectant 30% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.885 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 3.8→20 Å / Num. obs: 15932 / % possible obs: 99.1 % / Redundancy: 3.59 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.02
Reflection shellResolution: 3.8→3.9 Å / Rmerge(I) obs: 0.366 / Num. unique obs: 1094

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→19.929 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.903 / SU B: 27.574 / SU ML: 0.363 / Cross valid method: FREE R-VALUE / ESU R Free: 0.499
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2366 842 5.285 %
Rwork0.2117 15090 -
all0.213 --
obs-15932 98.895 %
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: 107.589 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20.97 Å20 Å2
2--1.94 Å2-0 Å2
3----6.292 Å2
Refinement stepCycle: LAST / Resolution: 3.8→19.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 411 67 0 4449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164123
X-RAY DIFFRACTIONr_angle_refined_deg0.7451.8686324
X-RAY DIFFRACTIONr_angle_other_deg0.2831.7649527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.351551
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.219511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05710702
X-RAY DIFFRACTIONr_dihedral_angle_6_deg9.67110206
X-RAY DIFFRACTIONr_chiral_restr0.0340.2693
X-RAY DIFFRACTIONr_chiral_restr_other0.0160.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
X-RAY DIFFRACTIONr_nbd_refined0.1690.2821
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.23769
X-RAY DIFFRACTIONr_nbtor_refined0.180.22033
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0650.226
X-RAY DIFFRACTIONr_nbd_other0.0960.2163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0370.216
X-RAY DIFFRACTIONr_mcbond_it1.90510.31940
X-RAY DIFFRACTIONr_mcbond_other1.90510.31940
X-RAY DIFFRACTIONr_mcangle_it3.38218.5232420
X-RAY DIFFRACTIONr_mcangle_other3.38118.5212421
X-RAY DIFFRACTIONr_scbond_it1.86711.6212657
X-RAY DIFFRACTIONr_scbond_other1.86711.622658
X-RAY DIFFRACTIONr_scangle_it3.40721.353904
X-RAY DIFFRACTIONr_scangle_other3.40721.3473905
X-RAY DIFFRACTIONr_lrange_it7.062111.5964904
X-RAY DIFFRACTIONr_lrange_other7.061111.614905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.8-3.8950.356700.29810590.30111390.9140.93599.1220.265
3.895-3.9970.286610.28510200.28510840.9470.92999.72330.247
3.997-4.1080.316530.2610340.26310910.9360.95199.63340.226
4.108-4.2290.305600.2489740.25110380.9420.95899.61460.205
4.229-4.3610.265570.2229440.22510060.9590.96799.5030.18
4.361-4.5070.267520.2149360.2179910.9560.96899.69730.173
4.507-4.6680.193550.2048970.2049540.9760.97399.79040.157
4.668-4.8470.217550.1918590.1929160.9630.97699.78170.144
4.847-5.0490.17490.1848370.1848870.980.97799.88730.141
5.049-5.2790.212370.1878330.1888710.9670.97399.88520.143
5.279-5.5430.261350.2247870.2268230.9560.96699.87850.176
5.543-5.8510.245310.2357340.2357650.9680.9661000.178
5.851-6.2170.219390.2277070.2267460.9680.9661000.183
6.217-6.6610.231300.2186600.2196910.9710.97199.85530.16
6.661-7.2160.184410.1666040.1686450.9820.9821000.137
7.216-7.9390.212270.1745640.1755910.9730.9811000.15
7.939-8.9340.154220.1545210.1545430.9860.9841000.138
8.934-10.430.233250.1764390.1794650.9730.98199.78490.169
10.43-13.0690.151240.1743890.1734130.9880.981000.175
13.069-19.9290.325190.2542920.2583140.9480.95699.04460.246

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