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- PDB-1h3f: Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1h3f
TitleTyrosyl-tRNA synthetase from Thermus thermophilus complexed with tyrosinol
ComponentsTYROSYL-TRNA SYNTHETASE
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / ATP + L-TYROSINE + TRNA(TYR)->AMP + PPI + L-TYROSYL-TRNA(TY CLASS I AMINOACYL-TRNA SYNTHETASE
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 / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / RNA-binding S4 domain / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / HUPs ...Tyrosine-tRNA ligase, bacterial-type, type 2 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / RNA-binding S4 domain / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / RNA-binding S4 domain superfamily / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-[(2S)-2-amino-3-hydroxypropyl]phenol / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCusack, S. / Yaremchuk, A. / Kriklivyi, I. / Tukalo, M.
CitationJournal: Embo J. / Year: 2002
Title: Class I Tyrosyl-tRNA Synthetase Has a Class II Mode or tRNA Recognition
Authors: Yaremchuk, A. / Kriklivyi, I. / Tukalo, M. / Cusack, S.
History
DepositionAug 28, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 17, 2018Group: Data collection / Structure summary / Category: chem_comp
Item: _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _chem_comp.type
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSYL-TRNA SYNTHETASE
B: TYROSYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3879
Polymers97,5722
Non-polymers8157
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-101 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.794, 111.050, 141.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999264, -0.012762, -0.036174), (-0.010661, -0.998277, 0.057691), (-0.036848, -0.057263, -0.997679)0.7865, 109.187, -7.7164
2given(-0.110243, -0.947442, 0.300333), (-0.993109, 0.092916, -0.071425), (0.039765, -0.306138, -0.951156)22.8835, 30.0757, 5.7826

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Components

#1: Protein TYROSYL-TRNA SYNTHETASE / TYROSINE--TRNA LIGASE


Mass: 48786.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83453, tyrosine-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TYE / 4-[(2S)-2-amino-3-hydroxypropyl]phenol / tyrosinol / bound form of TYROSINAL


Type: L-peptide linking / Mass: 167.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ATP + L-TYROSINE + TRNA(TYR) = AMP + DIPHOSPHATE + L-TYROSYL-TRNA(TYR). ...CATALYTIC ACTIVITY: ATP + L-TYROSINE + TRNA(TYR) = AMP + DIPHOSPHATE + L-TYROSYL-TRNA(TYR). ALTHOUGH THIS PROTEIN IS A CLASS I AMINOACYL-TRNA SYNTHETASE, IT DISPLAYS A CLASS II MODE OF TRNA RECOGNITION.
Sequence detailsUNMODELLED REGIONS DUE TO DISORDER: CHAIN A: 1-4, 80-100, 348-351 CHAIN B: 1-4, 84-96, 345-352

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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: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growpH: 5.8
Details: 12MG/ML PROTEIN IN 1:1 RATIO WITH RESERVOIR SOLUTION CONTAINING 1.2M AMMONIUM SULPHATE, 50MM MES(PH5.8), 10MM MGCL2, 0.5MM DDT, pH 5.80
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
21.2 Mammonium sulfate1reservoir
310 mM1reservoirMgCl2
40.5 mMdithiothreitol1reservoir
550 mMMES1reservoirpH5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 70951 / % possible obs: 97.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.3 / % possible all: 84.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 464280
Reflection shell
*PLUS
% possible obs: 84.5 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. THERMOPHILUS TYROSYL-TRNA SYNTHETASE PREVIOUSLY DETERMINED BY SIRAS BY SAME AUTHORS

Resolution: 2→25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1834546.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CHAIN A RESIDUES 1-4, 80-100 AND 348-351 AND CHAIN B RESIDUES 1-4, 84-96 AND 345-352 WERE UNMODELED DUE TO DISORDER
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3559 5 %RANDOM
Rwork0.234 ---
obs0.234 70950 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6936 Å2 / ksol: 0.38785 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å20 Å2
2--8.79 Å20 Å2
3----4.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 0 49 254 6777
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.691.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it3.733
X-RAY DIFFRACTIONc_scangle_it5.254
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 523 5.1 %
Rwork0.28 9832 -
obs--86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 3557 / % reflection Rfree: 4.9 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor Rwork: 0.28

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