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- PDB-1h3e: Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1h3e
TitleTyrosyl-tRNA synthetase from Thermus thermophilus complexed with wild-type tRNAtyr(GUA) and with ATP and tyrosinol
Components
  • TYROSYL-TRNA SYNTHETASE
  • WILD-TYPE TRNATYR(GUA)
KeywordsLIGASE / CLASS I AMINOACYL-TRNA SYNTHETASE: ATP + L-TYROSINE + TRNA(TYR) -> AMP + PPI + L-TYROSYL-TRNA(TYR)
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytoplasm
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 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / 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 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / RNA-binding S4 domain superfamily / S4 RNA-binding domain profile. / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 4-[(2S)-2-amino-3-hydroxypropyl]phenol / RNA / RNA (> 10) / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.0Oct 27, 2002Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 19, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
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 1.4Oct 30, 2019Group: Data collection / Derived calculations / Other / Category: pdbx_database_status / struct_conn / Item: _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSYL-TRNA SYNTHETASE
B: WILD-TYPE TRNATYR(GUA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1704
Polymers76,4962
Non-polymers6742
Water23413
1
A: TYROSYL-TRNA SYNTHETASE
B: WILD-TYPE TRNATYR(GUA)
hetero molecules

A: TYROSYL-TRNA SYNTHETASE
B: WILD-TYPE TRNATYR(GUA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,3408
Polymers152,9914
Non-polymers1,3494
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_646y+1,x-1,-z+11
Buried area14440 Å2
ΔGint-110.8 kcal/mol
Surface area55830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.525, 129.525, 109.451
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHE TETRAMER IS ACTUALLY A DIMER OF CHAIN A, EACH ASSOCIATED WITH A MOLECULE OF CHAIN B GIVING RISE TO A TETRAMERIC STATE

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Components

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


Mass: 48786.203 Da / Num. of mol.: 1
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: RNA chain WILD-TYPE TRNATYR(GUA)


Mass: 27709.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria)
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-TYE / 4-[(2S)-2-amino-3-hydroxypropyl]phenol / tyrosinol, bound form of TYROSINAL / Tyrosinol


Type: L-peptide linking / Mass: 167.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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.

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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: 3.63 Å3/Da / Density % sol: 65.8 %
Crystal growpH: 7
Details: DROP: 5MG/ML TYRRSTT+TRNA(TYR)WITH 5MM TYROSINOL, 10MM MGCL2, 10MM ATP, 50MM HEPES (PH7.0), 0.8M AMMONIUM SULPHATE. RESERVOIR: 1.5-1.6M AMMONIUM SULPHATE, 100MM HEPES (PH7.0)., pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.9→23 Å / Num. obs: 22669 / % possible obs: 94.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 115.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 5.9
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.5 / % possible all: 63.8

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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: 2.9→22.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1216869.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BASES OF TRNA NUCLEOTIDES 16,20,474, 74 OMITTED: NOT VISIBLE IN ELECTRON DENSITY. UNIDENTIFIED MODIFIED BASES IN THE TRNA(E.G ADE-37 IN CHAIN B) HAVE NOT BEEN MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1149 5.1 %RANDOM
Rwork0.219 ---
obs0.219 22644 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8415 Å2 / ksol: 0.337167 e/Å3
Displacement parametersBiso mean: 77.3 Å2
Baniso -1Baniso -2Baniso -3
1-10.06 Å222.22 Å20 Å2
2--10.06 Å20 Å2
3----20.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.9→22.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 1762 43 13 5221
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it5.353
X-RAY DIFFRACTIONc_scangle_it8.154
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 155 5.3 %
Rwork0.367 2774 -
obs--74.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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