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- PDB-1wz2: The crystal structure of Leucyl-tRNA synthetase and tRNA(leucine)... -

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Basic information

Entry
Database: PDB / ID: 1wz2
TitleThe crystal structure of Leucyl-tRNA synthetase and tRNA(leucine) complex
Components
  • Leucyl-tRNA synthetase
  • tRNATransfer RNA
KeywordsLigase/RNA / Ligase / tRNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / Ligase-RNA COMPLEX
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm
Similarity search - Function
leucyl-tRNA synthetase / Class I aminoacyl-tRNA synthetases (RS) / Leucine-tRNA ligase, archaeal / Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic / hypothetical protein PF0899 fold / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia ...leucyl-tRNA synthetase / Class I aminoacyl-tRNA synthetases (RS) / Leucine-tRNA ligase, archaeal / Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic / hypothetical protein PF0899 fold / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsFukunaga, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: The crystal structure of Leucyl-tRNA synthetase and tRNA(leucine) complex
Authors: Fukunaga, R. / Yokoyama, S.
History
DepositionFeb 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: tRNA
D: tRNA
A: Leucyl-tRNA synthetase
B: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)284,9994
Polymers284,9994
Non-polymers00
Water0
1
C: tRNA
A: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)142,4992
Polymers142,4992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: tRNA
B: Leucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)142,4992
Polymers142,4992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.546, 231.127, 118.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain tRNA / Transfer RNA


Mass: 28376.889 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Leucyl-tRNA synthetase / / Leucine--tRNA ligase / LeuRS


Mass: 114122.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: leuS / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58698, leucine-tRNA ligase

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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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% isopropanol, 200mM tri-sodium citrate, 100mM sodium cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1isopropanol11
2tri-sodium citrate11
3sodium cacodylate buffer11
4HOH11
5tri-sodium citrate12
6sodium cacodylate buffer12
7HOH12

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Data collection

DiffractionMean temperature: 173 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
ReflectionBiso Wilson estimate: 66.1 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→14.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2991506.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.305 4960 10.1 %RANDOM
Rwork0.241 ---
obs0.241 49242 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.5457 Å2 / ksol: 0.233691 e/Å3
Displacement parametersBiso mean: 84.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---6.45 Å20 Å2
3---6.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.21→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15818 3760 0 0 19578
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.61
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it2.442.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 669 10.1 %
Rwork0.315 5961 -
obs--74 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4DNA-RNA.PARAMDNA-RNA.TOP

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