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- PDB-1zjw: Glutaminyl-tRNA synthetase complexed to glutamine and 2'deoxy A76... -

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Basic information

Entry
Database: PDB / ID: 1zjw
TitleGlutaminyl-tRNA synthetase complexed to glutamine and 2'deoxy A76 glutamine tRNA
Components
  • Glutaminyl-tRNA
  • Glutaminyl-tRNA synthetaseQARS
KeywordsLIGASE/RNA / Protein-RNA complex / 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 / : / tRNA synthetases class I (E and Q), 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 / : / 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 / 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 MONOPHOSPHATE / GLUTAMINE / RNA / RNA (> 10) / Glutamine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsGruic-Sovulj, I. / Uter, N. / Bullock, T. / Perona, J.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: tRNA-dependent Aminoacyl-adenylate Hydrolysis by a Nonediting Class I Aminoacyl-tRNA Synthetase.
Authors: Gruic-Sovulj, I. / Uter, N. / Bullock, T. / Perona, J.J.
History
DepositionMay 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glutaminyl-tRNA
A: Glutaminyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2196
Polymers87,5342
Non-polymers6854
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)238.665, 93.465, 114.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain Glutaminyl-tRNA


Mass: 24099.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcribed RNA
#2: Protein Glutaminyl-tRNA synthetase / QARS / 6.1.1.18 / Glutamine--tRNA ligase / GlnRS


Mass: 63434.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glnS / Plasmid: PSJW1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS / References: UniProt: P00962, glutamine-tRNA ligase

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Non-polymers , 4 types, 146 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 3.8 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Ammonium Sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2H2O11
3Ammonium Sulfate12
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jul 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→60.58 Å / Num. obs: 56902 / % possible obs: 99.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 6.4
Reflection shellHighest resolution: 2.3 Å / % possible obs: 99.1 % / Num. measured obs: 4137

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
CNS1.1refinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→60 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.249 2252 5 %
Rwork0.22 --
all0.2211 --
obs0.2211 44486 99.5 %
Solvent computationBsol: 62.035 Å2
Displacement parametersBiso mean: 50.174 Å2
Baniso -1Baniso -2Baniso -3
1--12.069 Å20 Å20 Å2
2--5.902 Å20 Å2
3---6.168 Å2
Refinement stepCycle: LAST / Resolution: 2.5→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 1569 43 142 6033
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5ligand.par

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