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- PDB-1tke: Crystal structure of the editing domain of threonyl-tRNA syntheta... -

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Basic information

Entry
Database: PDB / ID: 1tke
TitleCrystal structure of the editing domain of threonyl-tRNA synthetase complexed with serine
ComponentsThreonyl-tRNA synthetase
KeywordsLIGASE
Function / homology
Function and homology information


tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / regulation of translation / tRNA binding / response to antibiotic / protein homodimerization activity / RNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / Threonyl/alanyl tRNA synthetase, SAD / TGS domain ...Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / Threonyl/alanyl tRNA synthetase, SAD / TGS domain / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Beta-grasp domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Beta-grasp domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SERINE / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsDock-Bregeon, A.C. / Rees, B. / Torres-Larios, A. / Bey, G. / Caillet, J. / Moras, D.
CitationJournal: Mol.Cell / Year: 2004
Title: Achieving Error-Free Translation; The Mechanism of Proofreading of Threonyl-tRNA Synthetase at Atomic Resolution.
Authors: Dock-Bregeon, A.C. / Rees, B. / Torres-Larios, A. / Bey, G. / Caillet, J. / Moras, D.
History
DepositionJun 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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
A: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5712
Polymers25,4661
Non-polymers1051
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.697, 44.913, 116.607
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 Threonyl-tRNA synthetase / Threonine--tRNA ligase / ThrRS


Mass: 25465.930 Da / Num. of mol.: 1 / Fragment: Domains N1 and N2 (residues 1-224)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: THRS, B1719, C2116, SF1512, S1630 / Plasmid: peT28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A8M3, threonine-tRNA ligase
#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Tris.cl, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2003
RadiationMonochromator: Si111 or Si311 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.46→24.5 Å / Num. all: 40336 / Num. obs: 40336 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.041
Reflection shellResolution: 1.46→1.52 Å / Rmerge(I) obs: 0.129 / Num. unique all: 3915 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QF6

1qf6


Resolution: 1.46→24.45 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1293636.7 / 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
Rfree0.207 2017 5 %RANDOM
Rwork0.178 ---
all0.18 40336 --
obs0.18 40336 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.806 Å2 / ksol: 0.408883 e/Å3
Displacement parametersBiso mean: 12.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.7 Å20 Å2
3----0.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.14 Å
Luzzati d res low-4 Å
Refinement stepCycle: LAST / Resolution: 1.46→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 7 409 2220
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.532
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 1.46→1.51 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.207 200 5.5 %
Rwork0.181 3453 -
obs-3653 91.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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