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- PDB-1qru: GLUTAMINYL-TRNA SYNTHETASE MUTANT I129T COMPLEXED WITH GLUTAMINE ... -

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Basic information

Entry
Database: PDB / ID: 1qru
TitleGLUTAMINYL-TRNA SYNTHETASE MUTANT I129T COMPLEXED WITH GLUTAMINE TRANSFER RNA
Components
  • PROTEIN (GLUTAMINYL-TRNA SYNTHETASE (E.C.6.1.1.18))
  • TRNAGLN2
KeywordsLIGASE/RNA / AMINOACYL-TRNA SYNTHASE / PROTEIN BIOSYNTHESIS / LIGASE / ATP-B / COMPLEX (AMINOACYL-TRNA SYNTHASE-TRNA) / 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 / : / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Ribosomal Protein L25; Chain P / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain ...Glutamine-tRNA ligase, bacterial / Glutamine-tRNA synthetase / Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Ribosomal Protein L25; Chain P / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Ribosomal Protein L25; Chain P / 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. / HUPs / 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 / Alpha-Beta Complex / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Glutamine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsArnez, J.G. / Steitz, T.A.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP.
Authors: Arnez, J.G. / Steitz, T.A.
#1: Journal: Nature / Year: 1991
Title: Structural Basis of Anticodon Loop Recognition by Glutaminyl-tRNA Synthetase
Authors: Rould, M.A. / Perona, J.J. / Steitz, T.A.
#2: 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. / Soll, D.
#3: 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.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Transfer RNA Mischarging Mediated by a Mutant Escherichia Coli Glutaminyl-tRNA Synthetase
Authors: Inokuchi, H. / Hoben, P. / Yamao, F. / Ozeki, H. / Soll, D.
History
DepositionJun 14, 1996Processing site: NDB
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: TRNAGLN2
A: PROTEIN (GLUTAMINYL-TRNA SYNTHETASE (E.C.6.1.1.18))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9903
Polymers87,4832
Non-polymers5071
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)242.000, 93.700, 115.500
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 TRNAGLN2 / GLUTAMINE TRANSFER RNA


Mass: 24060.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Description: LAMBDA PL PROMOTER / Gene: TRNAGLN2 / Variant: DELTAH1DELTATRP / Plasmid details: PLC28 DERIVATIVE / Plasmid: PRS3 (PLC28 DERIVATIVE) / Gene (production host): TRNAGLN2 / Production host: Escherichia coli (E. coli)
#2: Protein PROTEIN (GLUTAMINYL-TRNA SYNTHETASE (E.C.6.1.1.18)) / GLUTAMINYL-TRNA LIGASE


Mass: 63422.586 Da / Num. of mol.: 1 / Mutation: I129T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: X3R2 (GLNS DELETION STRAIN) / Description: GLNS PROMOTER (NO OVEREXPRESSION) / Gene: GLNS15 / Plasmid details: DERIVATIVE OF PBR / Plasmid: PRS12 (DERIVATIVE OF PBR322) / Gene (production host): GLNS15 / Production host: Escherichia coli (E. coli) / Keywords: MUTANT I129T / References: UniProt: P00962, glutamine-tRNA ligase
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 70 %
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
280 mMPIPES1reservoir
320 mM1reservoirMgSO4
40.02 %1reservoirNaN3
51.8-2.0 Mammonium sulfate1reservoir
68 mMATP1reservoir

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Data collection

DetectorType: SDMS / Detector: AREA DETECTOR / Date: Dec 1, 1989
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 23275 / % possible obs: 90.7 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.097
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 9 Å / % possible obs: 90.7 % / Observed criterion σ(I): 0 / Redundancy: 2.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
SDMSdata reduction
RefinementResolution: 3→7 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.23 -
obs0.23 22183
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 1802 34 14 7104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.65
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
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 7 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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