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- PDB-5omw: Mutant T252A of E. coli leucyl-tRNA synthetase, tRNA(leu) and leu... -

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Basic information

Entry
Database: PDB / ID: 5omw
TitleMutant T252A of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucyl-adenylate analogue in the aminoacylation conformation
Components
  • L-leucyl-tRNA
  • Leucine--tRNA ligase
KeywordsTRANSLATION / reaction catalysed: ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) protein translation / aminoacyl-tRNA activity / leucine-tRNA ligase / class Ia
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing 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
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: 2.6 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 1.1Dec 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 1.2Jun 13, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._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 / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rsym_value ..._reflns.pdbx_CC_half / _reflns.pdbx_Rsym_value / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rsym_value / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all
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: L-leucyl-tRNA
D: Leucine--tRNA ligase
E: L-leucyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,17610
Polymers255,0774
Non-polymers1,0986
Water00
1
A: Leucine--tRNA ligase
B: L-leucyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0885
Polymers127,5392
Non-polymers5493
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-98 kcal/mol
Surface area47310 Å2
MethodPISA
2
D: Leucine--tRNA ligase
E: L-leucyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0885
Polymers127,5392
Non-polymers5493
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-97 kcal/mol
Surface area47390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.250, 68.910, 228.330
Angle α, β, γ (deg.)90.00, 104.93, 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 L-leucyl-tRNA


Mass: 28052.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: T7 in vitro transcription / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1207385735
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.36 Å3/Da / Density % sol: 47.84 % / Description: 2D needles
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→220.62 Å / Num. obs: 73538 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rsym value: 0.121 / Net I/σ(I): 7.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.69 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.66 / Rsym value: 0.763 / % possible all: 99.9

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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: 2.6→220.62 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.696 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 2.094 / ESU R Free: 0.346 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26416 3665 5 %RANDOM
Rwork0.21867 ---
obs0.22092 69873 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.24 Å2
2--0.37 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.6→220.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13666 3409 66 0 17141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01817859
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214418
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.79425011
X-RAY DIFFRACTIONr_angle_other_deg0.973333628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67351718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23124.551668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.271152380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5931582
X-RAY DIFFRACTIONr_chiral_restr0.0660.22706
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023720
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_it2.0926.0316884
X-RAY DIFFRACTIONr_mcbond_other2.0926.0316884
X-RAY DIFFRACTIONr_mcangle_it3.6229.0448598
X-RAY DIFFRACTIONr_mcangle_other3.6229.0448599
X-RAY DIFFRACTIONr_scbond_it1.8686.19310975
X-RAY DIFFRACTIONr_scbond_other1.8686.19310976
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1749.25316414
X-RAY DIFFRACTIONr_long_range_B_refined5.17764.33119750
X-RAY DIFFRACTIONr_long_range_B_other5.17764.3319751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 260 -
Rwork0.382 5129 -
obs--99.81 %

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