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- PDB-2dxi: 2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 2dxi
Title2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol
Components
  • glutamyl-tRNA synthetase
  • tRNA
Keywordsligase/RNA / LIGASE / RNA / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ligase-RNA COMPLEX
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Aminoacyl-tRNA synthetase, class I, anticodon-binding / Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 / Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1 / Arc Repressor Mutant, subunit A - #350 / Glutamate-tRNA ligase, bacterial/mitochondrial / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Glutamyl-tRNA synthetase / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Glutamyl-tRNA Synthetase; domain 2 ...Aminoacyl-tRNA synthetase, class I, anticodon-binding / Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 / Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1 / Arc Repressor Mutant, subunit A - #350 / Glutamate-tRNA ligase, bacterial/mitochondrial / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Glutamyl-tRNA synthetase / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / 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 / Helicase, Ruva Protein; domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / (4S)-4-AMINO-5-HYDROXYPENTANOIC ACID / RNA / RNA (> 10) / Glutamate--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSekine, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2006
Title: Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase
Authors: Sekine, S. / Shichiri, M. / Bernier, S. / Chenevert, R. / Lapointe, J. / Yokoyama, S.
History
DepositionAug 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: tRNA
D: tRNA
A: glutamyl-tRNA synthetase
B: glutamyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,51710
Polymers156,1884
Non-polymers1,3296
Water6,467359
1
C: tRNA
A: glutamyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7595
Polymers78,0942
Non-polymers6653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: tRNA
B: glutamyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7595
Polymers78,0942
Non-polymers6653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.615, 219.119, 135.816
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, 4 molecules CDAB

#1: RNA chain tRNA


Mass: 24105.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: In vitro transcription
#2: Protein glutamyl-tRNA synthetase / Glutamate--tRNA ligase / Glurs


Mass: 53988.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PK7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27000, glutamate-tRNA ligase

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Non-polymers , 4 types, 365 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-GAU / (4S)-4-AMINO-5-HYDROXYPENTANOIC ACID / L-GLUTAMOL


Type: L-peptide linking / Mass: 133.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG1500, MOPS-NA, AMMONIUM SULFATE, MPD, pH 6.70, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG150011
2Mops-Na11
3ammonium sulfate11
4MPD11
5HOH11
6PEG150012
7ammonium sulfate12
8MPD12
9HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2004
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 94855 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 19.2
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.89 / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N78

1n78


Resolution: 2.2→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4358199.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4167 5 %RANDOM
Rwork0.214 ---
obs0.214 83516 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.57 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.16 Å20 Å20 Å2
2---9.73 Å20 Å2
3---2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7628 3194 91 359 11272
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d1.59
X-RAY DIFFRACTIONc_mcbond_it3.881.5
X-RAY DIFFRACTIONc_mcangle_it4.892
X-RAY DIFFRACTIONc_scbond_it5.632
X-RAY DIFFRACTIONc_scangle_it6.972.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.322 409 4.9 %
Rwork0.263 7875 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION4ligand.paramligand.top
X-RAY DIFFRACTION5ion.paramion.top

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