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- PDB-5on3: Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthet... -

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Basic information

Entry
Database: PDB / ID: 5on3
TitleQuaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of leucine in the aminoacylation conformation
Components
  • Leucine--tRNA ligase
  • tRNA(leu)
KeywordsLIGASE / reaction catalysed: ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) protein translation / aminoacyl-tRNA activity / leucine-tRNA ligase / class Ia / TRANSLATION
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / 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
Similarity search - Domain/homology
Chem-9YN / 5'-O-(L-leucylsulfamoyl)adenosine / : / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPalencia, A. / Cusack, S.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.
Authors: Dulic, M. / Cvetesic, N. / Zivkovic, I. / Palencia, A. / Cusack, S. / Bertosa, B. / Gruic-Sovulj, I.
History
DepositionAug 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.5Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine--tRNA ligase
B: tRNA(leu)
D: Leucine--tRNA ligase
E: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,8209
Polymers255,0774
Non-polymers1,7435
Water00
1
A: Leucine--tRNA ligase
B: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4435
Polymers127,5392
Non-polymers9043
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-49 kcal/mol
Surface area46750 Å2
MethodPISA
2
D: Leucine--tRNA ligase
E: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3784
Polymers127,5392
Non-polymers8392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-44 kcal/mol
Surface area47670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.000, 68.700, 227.200
Angle α, β, γ (deg.)90.00, 102.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 99485.992 Da / Num. of mol.: 2 / Mutation: T252A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: leuS, b0642, JW0637 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain tRNA(leu)


Mass: 28052.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: T7 in vitro transcribed / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1208670917
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O7S
#5: Chemical ChemComp-9YN / (2~{S})-~{N}-[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-4-methyl-pentanamide


Mass: 379.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O4

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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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS PH 5.5, 23-25% W/V PEG 3350, AND 200 MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 43333 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.97 / Rsym value: 0.02 / Net I/σ(I): 5.2
Reflection shellResolution: 3.1→3.23 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4935 / CC1/2: 0.39 / Rsym value: 1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AQ7

4aq7


Resolution: 3.1→221.55 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.859 / SU B: 33.345 / SU ML: 0.546 / Cross valid method: THROUGHOUT / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27753 2144 4.9 %RANDOM
Rwork0.24113 ---
obs0.24293 41189 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0 Å2-1.32 Å2
2--3.85 Å20 Å2
3----2.05 Å2
Refinement stepCycle: 1 / Resolution: 3.1→221.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13594 3350 117 0 17061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01817780
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214366
X-RAY DIFFRACTIONr_angle_refined_deg0.8951.79924896
X-RAY DIFFRACTIONr_angle_other_deg0.886333496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.91951707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19324.535666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.729152364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1271582
X-RAY DIFFRACTIONr_chiral_restr0.0530.22694
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02117491
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023707
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9557.1286849
X-RAY DIFFRACTIONr_mcbond_other0.9557.1286849
X-RAY DIFFRACTIONr_mcangle_it1.77710.698549
X-RAY DIFFRACTIONr_mcangle_other1.77710.6918550
X-RAY DIFFRACTIONr_scbond_it0.717.31910931
X-RAY DIFFRACTIONr_scbond_other0.717.31910932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.29710.98816348
X-RAY DIFFRACTIONr_long_range_B_refined2.84778.47220142
X-RAY DIFFRACTIONr_long_range_B_other2.84778.47120143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 154 -
Rwork0.378 3007 -
obs--98.32 %

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