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- PDB-1jh3: Solution structure of tyrosyl-tRNA synthetase C-terminal domain. -

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Basic information

Entry
Database: PDB / ID: 1jh3
TitleSolution structure of tyrosyl-tRNA synthetase C-terminal domain.
ComponentsTYROSYL-TRNA SYNTHETASE
KeywordsLIGASE / aminoacyl-tRNA synthetase / anticodon-arm binding domain
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / regulation of protein complex stability / tRNA binding / protein homodimerization activity / protein-containing complex / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / 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) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold ...Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / 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) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing
AuthorsGuijarro, J.I. / Pintar, A. / Prochnicka-Chalufour, A. / Guez, V. / Gilquin, B. / Bedouelle, H. / Delepierre, M.
Citation
Journal: Structure / Year: 2002
Title: Structure and Dynamics of the Anticodon Arm Binding Domain of Bacillus stearothermophilus Tyrosyl-tRNA Synthetase
Authors: Guijarro, J.I. / Pintar, A. / Prochnicka-Chalufour, A. / Guez, V. / Gilquin, B. / Bedouelle, H. / Delepierre, M.
#1: Journal: FEBS Lett. / Year: 1999
Title: Secondary structure of the C-terminal domain of the tyrosyl-transfer RNA synthetase from Bacillus stearothermophilus: a novel type of anticodon binding domain?
Authors: Pintar, A. / Guez, V. / Castagne, C. / Bedouelle, H. / Delepierre, M.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)12,0021
Polymers12,0021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TYROSYL-TRNA SYNTHETASE


Mass: 12001.544 Da / Num. of mol.: 1 / Fragment: C-terminal domain (Residues 321-419)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: tyrS / Plasmid: PET-20b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00952, tyrosine-tRNA ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1232D NOESY
131HMQC-J

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM protein, U-15N20mM potassium phosphate, 90% H2O, 10% D2O
20.8mM protein, U-15N, U-13C20mM potassium phosphate, 90% H2O, 10% D2O
31.0mM protein20mM potassium phosphate, 100% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XEASY1.2Bartels, Xia, Billeter, Guntertdata analysis
DYANA1.5Guntert, Mumenthaler, Herrmannstructure solution
OPAL2.6Luginbuhl, Guntert, Billeterrefinement
VNMR6.1bcollection
RefinementMethod: torsion angle dynamics simulated annealing / Software ordinal: 1
Details: Structures were calculated using 1352 meaningful upper distance restraints, 71 dihedral angle restraints and 33 hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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