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- PDB-4ari: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -

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Basic information

Entry
Database: PDB / ID: 4ari
TitleTernary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and the benzoxaborole AN2679 in the editing conformation
Components
  • LEUCINE--TRNA LIGASE
  • TRNA-LEU5 (UAA ISOACEPTOR)
KeywordsLIGASE/RNA / LIGASE-RNA COMPLEX / LIGASE / NUCLEOTIDE(ATP)-BINDING / PROTEIN BIOSYNTHESIS / CLASS I AMINOACYL-TRNA SYNTHETASE
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
Rubrerythrin, domain 2 - #290 / Ubiquitin-like (UB roll) - #590 / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia ...Rubrerythrin, domain 2 - #290 / Ubiquitin-like (UB roll) - #590 / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Rubrerythrin, domain 2 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Single Sheet / Rossmann-like alpha/beta/alpha sandwich fold / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsPalencia, A. / Crepin, T. / Vu, M.T. / Lincecum Jr, T.L. / Martinis, S.A. / Cusack, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-tRNA Synthetase
Authors: Palencia, A. / Crepin, T. / Vu, M.T. / Lincecum Jr, T.L. / Martinis, S.A. / Cusack, S.
History
DepositionApr 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Jul 25, 2012Group: Database references
Revision 2.0May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_proc ...entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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: LEUCINE--TRNA LIGASE
B: TRNA-LEU5 (UAA ISOACEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1018
Polymers127,6842
Non-polymers4176
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-57 kcal/mol
Surface area46940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.180, 118.940, 141.030
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 LEUCINE--TRNA LIGASE / LEUCYL-TRNA SYNTHETASE / LEURS


Mass: 99516.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain TRNA-LEU5 (UAA ISOACEPTOR)


Mass: 28167.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: UNMODIFIED T7 TRANSCRIPT / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.5 Å3/Da / Density % sol: 49.8 % / Description: NONE
Crystal growpH: 5.6
Details: THE TERNARY COMPLEX ECLEURS-TRNA-AN2679 WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE (PH 5.6), 14-18% (W/V) PEG 6000 AND 20 MM NACL. THE CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING 22% (V/V) ...Details: THE TERNARY COMPLEX ECLEURS-TRNA-AN2679 WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE (PH 5.6), 14-18% (W/V) PEG 6000 AND 20 MM NACL. THE CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING 22% (V/V) ETHYLENE GLYCOL AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 74893 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.91 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.1
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / % possible all: 74.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3N

1h3n


Resolution: 2.08→90.91 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.66 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24436 3759 5 %RANDOM
Rwork0.19879 ---
obs0.2011 71134 96.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.08→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 1720 26 324 8591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0188619
X-RAY DIFFRACTIONr_bond_other_d0.0010.025315
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.8412076
X-RAY DIFFRACTIONr_angle_other_deg0.994312938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0165819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33124.465318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.542151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8191539
X-RAY DIFFRACTIONr_chiral_restr0.0980.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021794
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.082→2.136 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 199 -
Rwork0.273 3937 -
obs--74.24 %

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