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- PDB-1gsg: Structure of E.coli glutaminyl-tRNA synthetase complexed with trn... -

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Basic information

Entry
Database: PDB / ID: 1gsg
TitleStructure of E.coli glutaminyl-tRNA synthetase complexed with trnagln and ATP at 2.8 Angstroms resolution
Components
  • GLUTAMINYL-TRNA SYNTHETASEQARS
  • TRNAGLN
KeywordsLIGASE/RNA / PROTEIN-T-RNA COMPLEX / SINGLE STRAND / PROTEIN/RNA / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function
Glutamine-tRNA ligase, bacterial / Glutamine-tRNA synthetase / Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain ...Glutamine-tRNA ligase, bacterial / Glutamine-tRNA synthetase / Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Glutamine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsRould, M.A. / Perona, J.J. / Soell, D. / Steitz, T.A.
Citation
Journal: Science / Year: 1989
Title: Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution.
Authors: Rould, M.A. / Perona, J.J. / Soll, D. / Steitz, T.A.
#1: Journal: Science / Year: 1989
Title: Structural Basis for Misaminoacylation by Mutant E. Coli Glutaminyl-tRNA Synthetase Enzymes
Authors: Perona, J.J. / Swanson, R.N. / Rould, M.A. / Steitz, T.A. / Soell, D.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Overproduction and Purification of Escherichia Coli tRNA(2Gln) and its Use in Crystallization of the Glutaminyl-tRNA Synthetase-tRNA(Gln) Complex
Authors: Perona, J.J. / Swanson, R. / Steitz, T.A. / Soell, D.
History
DepositionApr 3, 1990Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 24, 1992Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Other
Revision 1.4May 9, 2012Group: Other
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: TRNAGLN
P: GLUTAMINYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)87,5692
Polymers87,5692
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)242.800, 93.600, 115.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain TRNAGLN / Coordinate model: P atoms only


Mass: 24134.473 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein GLUTAMINYL-TRNA SYNTHETASE / QARS / Coordinate model: Cα atoms only


Mass: 63434.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00962, glutamine-tRNA ligase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 202.121 1988 / PH range low: 7.2 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
180 mMPIPES1reservoir
220 mM1reservoirMgCl2
34 mMATP1reservoir
420 mMbeta-mercaptoethanol1reservoir
62.0 Mammonium sulfate1reservoir
5tRNA enzyme1drop

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Data collection

DetectorType: SDMS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.8 Å
Reflection
*PLUS
Lowest resolution: 18 Å / Num. obs: 31768 / Num. measured all: 152900 / Rmerge(I) obs: 0.044

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→7 Å / Rfactor Rwork: 0.279 / Rfactor obs: 0.279
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms526 75 0 0 601
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 7 Å / Rfactor all: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS

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