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- PDB-1wka: Structural basis for non-cognate amino acid discrimination by the... -

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Basic information

Entry
Database: PDB / ID: 1wka
TitleStructural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain
ComponentsValyl-tRNA synthetase
KeywordsLIGASE / editing / cp1 / valyl-trna synthetase / fidelity / thermus thrmophilus / translation / amino acid / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


valine-tRNA ligase / valine-tRNA ligase activity / valyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Valine-tRNA ligase / Valyl-tRNA synthetase, tRNA-binding arm / Valyl tRNA synthetase, anticodon-binding domain / Valyl tRNA synthetase tRNA binding arm / Valyl-tRNA synthetase, tRNA-binding arm superfamily / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) ...Valine-tRNA ligase / Valyl-tRNA synthetase, tRNA-binding arm / Valyl tRNA synthetase, anticodon-binding domain / Valyl tRNA synthetase tRNA binding arm / Valyl-tRNA synthetase, tRNA-binding arm superfamily / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFukunaga, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Basis for Non-cognate Amino Acid Discrimination by the Valyl-tRNA Synthetase Editing Domain
Authors: Fukunaga, R. / Yokoyama, S.
History
DepositionMay 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Valyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)16,6421
Polymers16,6421
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.960, 95.960, 71.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-78-

HOH

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Components

#1: Protein Valyl-tRNA synthetase / Valine--tRNA ligase / ValRS


Mass: 16641.943 Da / Num. of mol.: 1 / Fragment: CP1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P96142, valine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-HCl buffer (pH 8.0), 1.15M tri-sodium citrate, 5% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 22009 / Num. obs: 21991 / % possible obs: 99.9 % / Biso Wilson estimate: 19.7 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GAX

1gax


Resolution: 1.7→47.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2045641.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 963 4.4 %RANDOM
Rwork0.191 ---
obs0.191 21991 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.8541 Å2 / ksol: 0.367352 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å21.84 Å20 Å2
2--1.92 Å20 Å2
3----3.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.7→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 0 167 1312
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it2.851.5
X-RAY DIFFRACTIONc_mcangle_it3.622
X-RAY DIFFRACTIONc_scbond_it5.72
X-RAY DIFFRACTIONc_scangle_it7.832.5
LS refinement shellResolution: 1.7→1.81 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.299 3580 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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