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- PDB-1euy: GLUTAMINYL-TRNA SYNTHETASE COMPLEXED WITH A TRNA MUTANT AND AN AC... -

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Basic information

Entry
Database: PDB / ID: 1euy
TitleGLUTAMINYL-TRNA SYNTHETASE COMPLEXED WITH A TRNA MUTANT AND AN ACTIVE SITE INHIBITOR
Components
  • GLUTAMINYL TRNA
  • GLUTAMINYL-TRNA SYNTHETASE
Keywordsligase/RNA / TRNA SYNTHETASE / GLUTAMINE / TRNAGLN / E. COLI / 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 / 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
5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE / RNA / RNA (> 10) / Glutamine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsSherlin, L.D. / Bullock, T.L. / Newberry, K.J. / Lipman, R.S.A. / Hou, Y.-M. / Beijer, B. / Sproat, B.S. / Perona, J.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases.
Authors: Sherlin, L.D. / Bullock, T.L. / Newberry, K.J. / Lipman, R.S. / Hou, Y.M. / Beijer, B. / Sproat, B.S. / Perona, J.J.
History
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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)87,1863
Polymers86,7112
Non-polymers4741
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)235.20, 94.20, 113.41
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: RNA chain GLUTAMINYL TRNA


Mass: 23817.186 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Product of runoff T7 Polymerase transcription from synthetic DNA template
#2: Protein GLUTAMINYL-TRNA SYNTHETASE / E.C.6.1.1.18 / GLNRS / GLUTAMINE-TRNA LIGASE


Mass: 62894.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00962, glutamine-tRNA ligase
#3: Chemical ChemComp-QSI / 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE


Mass: 474.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N8O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.62 Å3/Da / Density % sol: 66.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.1 M (NH4)2SO4, 70 mM Buffer, 20 mM MgCl2, 20 mM BME at 298 K, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1Buffer11
2BME11
3MgCl211
4(NH4)2SO411
5MgCl212
6(NH4)2SO412
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
210 mMPIPES1drop
35 mMbeta-mercaptoethanol1drop
42-5 mg/mltRNA mutant1drop
55 mM1dropMgSO4
62 mMQSI1drop
72.1 Mammonium sulfate1reservoir
870 mMPIPES1reservoir
920 mM1reservoirMgCl2
1020 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98
DetectorType: OTHER / Detector: CCD / Date: Apr 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 48345 / Num. obs: 48345 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 0.151
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 1 % / Rmerge(I) obs: 0.274 / % possible all: 95.2
Reflection
*PLUS
Num. measured all: 309007
Reflection shell
*PLUS
% possible obs: 95.2 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 --RANDOM
Rwork0.234 ---
all-48345 --
obs-48345 95.5 %-
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4274 1555 32 54 5915
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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