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- PDB-1j09: Crystal structure of Thermus thermophilus glutamyl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 1j09
TitleCrystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu
ComponentsGlutamyl-tRNA synthetase
KeywordsLIGASE / GluRS-ATP-Glu complex / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytoplasm
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 / GLUTAMIC ACID / Glutamate--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSekine, S. / Nureki, O. / Dubois, D.Y. / Bernier, S. / Chenevert, R. / Lapointe, J. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: EMBO J. / Year: 2003
Title: ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding
Authors: Sekine, S. / Nureki, O. / Dubois, D.Y. / Bernier, S. / Chenevert, R. / Lapointe, J. / Vassylyev, D.G. / Yokoyama, S.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase
Authors: Sekine, S. / Nureki, O. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S.
#2: Journal: Science / Year: 1995
Title: Architectures of class-defining and specific domains of glutamyl-tRNA synthetase
Authors: Nureki, O. / Vassylyev, D.G. / Katayanagi, K. / Shimizu, T. / Sekine, S. / Kigawa, T. / Miyazawa, T. / Yokoyama, S. / Morikawa, K.
History
DepositionNov 12, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Glutamyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6674
Polymers53,9891
Non-polymers6793
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.920, 82.620, 83.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamyl-tRNA synthetase / GluRS / Glutamate--tRNA ligase


Mass: 53988.727 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.39 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 or 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.0 mg/mlprotein1drop
210 mMMOPS/Na1droppH6.5
35 mM1dropMgCl2
42.5 mM2-mercaptoethanol1drop
51 %PEG60001drop
62 mMATP1drop
72 mMglutamate1drop
810 %PEG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 11, 2001
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 49026 / Num. obs: 49026 / % possible obs: 91.7 % / Observed criterion σ(I): -1 / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.8→1.88 Å / Rmerge(I) obs: 0.444 / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 208385
Reflection shell
*PLUS
% possible obs: 92.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1GLN

1gln


Resolution: 1.8→37.12 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1790268.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2431 5 %RANDOM
Rwork0.199 ---
obs0.199 48560 91.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.4768 Å2 / ksol: 0.355014 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2--5.64 Å20 Å2
3----4.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 45 352 4211
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.311 288 4.7 %
Rwork0.283 5785 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ATP.PARAMLIGAND.TOP
X-RAY DIFFRACTION4MG.PARAMMG.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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