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- PDB-4as1: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -

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Basic information

Entry
Database: PDB / ID: 4as1
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 deacylase 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 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) ...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 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Isoleucyl-tRNA Synthetase; Domain 1 / 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: 2.02 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 27, 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 14, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)127,7083
Polymers127,6842
Non-polymers241
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-46.7 kcal/mol
Surface area48800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.680, 77.110, 91.140
Angle α, β, γ (deg.)90.00, 102.24, 90.00
Int Tables number4
Space group name H-MP1211

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.36 Å3/Da / Density % sol: 47.93 % / 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: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM Q120 / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 78307 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.65 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 2.81 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.6 / % possible all: 84.5

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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: 2.02→19.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.436 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24922 3977 5.1 %RANDOM
Rwork0.20799 ---
obs0.21007 74330 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.45 Å2
2---0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.02→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6458 1786 1 402 8647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0188629
X-RAY DIFFRACTIONr_bond_other_d0.0010.025297
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.83212111
X-RAY DIFFRACTIONr_angle_other_deg1.059312889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.324.469320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.918151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.241539
X-RAY DIFFRACTIONr_chiral_restr0.1090.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218410
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021807
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: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 246 -
Rwork0.344 4674 -
obs--84.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.55270.11730.5450.8560.03711.31760.00220.06340.01850.0252-0.116-0.0289-0.06-0.05120.11380.0451-0.00860.0240.0268-0.00870.034238.0349.45617.715
24.1391.1399-1.24715.634-1.15985.0518-0.0914-0.1583-0.4691-0.14230.07680.00040.5987-0.25750.01460.1493-0.07480.05420.3148-0.08890.209410.943-10.10516.987
33.39890.8176-0.42993.66690.93043.2966-0.06220.2115-0.0194-0.16090.0863-0.22960.27640.2645-0.02420.1750.03290.01690.1182-0.03640.121758.57-32.13931.602
42.67964.3994-2.40839.09-3.67443.35520.0803-0.10740.31270.26910.82321.25990.4018-0.2043-0.90360.2918-0.0271-0.15870.99670.60090.889-6.539-3.58137.027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 230
2X-RAY DIFFRACTION1A416 - 794
3X-RAY DIFFRACTION2B1 - 72
4X-RAY DIFFRACTION3A231 - 415
5X-RAY DIFFRACTION3B73 - 76
6X-RAY DIFFRACTION4A795 - 858

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