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- PDB-1gtr: STRUCTURAL BASIS OF ANTICODON LOOP RECOGNITION BY GLUTAMINYL-TRNA... -

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Basic information

Entry
Database: PDB / ID: 1gtr
TitleSTRUCTURAL BASIS OF ANTICODON LOOP RECOGNITION BY GLUTAMINYL-TRNA SYNTHETASE
Components
  • GLUTAMINYL-tRNA SYNTHETASEQARS
  • RNA (74-MER)
KeywordsCOMPLEX (LIGASE/TRNA) / COMPLEX (LIGASE-TRNA) / COMPLEX (LIGASE-TRNA) complex
Function / homologyRossmann-like alpha/beta/alpha sandwich fold / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / Aminoacyl-transfer RNA synthetases class-I signature. / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), catalytic domain / Glutamine-tRNA ligase, bacterial / Glutamyl/glutaminyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, conserved site / Glutamine-tRNA synthetase / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily ...Rossmann-like alpha/beta/alpha sandwich fold / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / Aminoacyl-transfer RNA synthetases class-I signature. / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), catalytic domain / Glutamine-tRNA ligase, bacterial / Glutamyl/glutaminyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, conserved site / Glutamine-tRNA synthetase / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / ATP binding / cytosol / Glutamine--tRNA ligase
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / 2.5 Å resolution
AuthorsRould, M.A. / Perona, J.J. / Steitz, T.A.
CitationJournal: Nature / Year: 1991
Title: Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase.
Authors: Rould, M.A. / Perona, J.J. / Steitz, T.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 15, 1993 / Release: Feb 7, 1995
RevisionDateData content typeGroupProviderType
1.0Feb 7, 1995Structure modelrepositoryInitial release
1.1May 22, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 16, 2011Structure modelAtomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA (74-MER)
A: GLUTAMINYL-tRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6963
Polyers87,1892
Non-polymers5071
Water4,161231
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)242.800, 94.300, 115.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21

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Components

#1: RNA chain RNA (74-MER)


Mass: 23754.121 Da / Num. of mol.: 1 / References: glutamine-tRNA ligase
#2: Protein/peptide GLUTAMINYL-tRNA SYNTHETASE / QARS


Mass: 63434.641 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P00962
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.8 / Density percent sol: 67.63 %
Crystal grow
*PLUS
Temp: 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
IDConcCommon nameCrystal IDSol IDChemical formula
180 mMPIPES1reservoir
220 mM1reservoirMgCl2
34 mMATP1reservoir
420 mMbeta-mercaptoethanol1reservoir
52.0 Mammonium sulfate1reservoir
6tRNA enzyme1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNumber obs: 37820 / Observed criterion sigma I: 0 / Percent possible obs: 84

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
Least-squares processR factor R work: 0.21 / R factor obs: 0.21 / Highest resolution: 2.5 Å / Lowest resolution: 6 Å
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 4279 / Nucleic acid: 1573 / Ligand: 31 / Solvent: 231 / Total: 6114
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Least-squares process
*PLUS
R factor R work: 0.21 / R factor obs: 0.21 / Number reflection obs: 37820
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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