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- PDB-3zjt: Ternary complex of E.coli leucyl-tRNA synthetase, tRNA(Leu)574 an... -

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Basic information

Entry
Database: PDB / ID: 3zjt
TitleTernary complex of E.coli leucyl-tRNA synthetase, tRNA(Leu)574 and the benzoxaborole AN3017 in the editing conformation
Components
  • LEUCYL-TRNA SYNTHETASE
  • TRNALEU5 UAA ISOACCEPTOR
KeywordsLIGASE/RNA / LIGASE-RNA COMPLEX / NUCLEOTIDE (ATP) -BINDING / PROTEIN BIOSYNTHESIS / CLASS I AMINOACYL-TRNA SYNTHETASE / AMINOACYL TRNA SYNTHETASE / ATP BINDING / EDITING 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)
ESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCusack, S. / Palencia, A. / Crepin, T. / Hernandez, V. / Akama, T. / Baker, S.J. / Bu, W. / Feng, L. / Freund, Y.R. / Liu, L. ...Cusack, S. / Palencia, A. / Crepin, T. / Hernandez, V. / Akama, T. / Baker, S.J. / Bu, W. / Feng, L. / Freund, Y.R. / Liu, L. / Meewan, M. / Mohan, M. / Mao, W. / Rock, F.L. / Sexton, H. / Sheoran, A. / Zhang, Y. / Zhang, Y. / Zhou, Y. / Nieman, J.A. / Anugula, M.R. / Keramane, E.M. / Savariraj, K. / Reddy, D.S. / Sharma, R. / Subedi, R. / Singh, R. / OLeary, A. / Simon, N.L. / DeMarsh, P.L. / Mushtaq, S. / Warner, M. / Livermore, D.M. / Alley, M.R.K. / Plattner, J.J.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Discovery of a Novel Class of Boron-Based Antibacterials with Activity Against Gram-Negative Bacteria.
Authors: Hernandez, V. / Crepin, T. / Palencia, A. / Cusack, S. / Akama, T. / Baker, S.J. / Bu, W. / Feng, L. / Freund, Y.R. / Liu, L. / Meewan, M. / Mohan, M. / Mao, W. / Rock, F.L. / Sexton, H. / ...Authors: Hernandez, V. / Crepin, T. / Palencia, A. / Cusack, S. / Akama, T. / Baker, S.J. / Bu, W. / Feng, L. / Freund, Y.R. / Liu, L. / Meewan, M. / Mohan, M. / Mao, W. / Rock, F.L. / Sexton, H. / Sheoran, A. / Zhang, Y. / Zhang, Y. / Zhou, Y. / Nieman, J.A. / Anugula, M.R. / Keramane, E.M. / Savariraj, K. / Reddy, D.S. / Sharma, R. / Subedi, R. / Singh, R. / O'Leary, A. / Simon, N.L. / De Marsh, P.L. / Mushtaq, S. / Warner, M. / Livermore, D.M. / Alley, M.R.K. / Plattner, J.J.
History
DepositionJan 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 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_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_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_comp_id / _struct_conn.ptnr2_auth_seq_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: LEUCYL-TRNA SYNTHETASE
B: TRNALEU5 UAA ISOACCEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1485
Polymers128,0752
Non-polymers733
Water4,936274
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-62.1 kcal/mol
Surface area47500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.900, 118.800, 140.400
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 LEUCYL-TRNA SYNTHETASE / 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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain TRNALEU5 UAA ISOACCEPTOR


Mass: 28558.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: UNMODIFIED T7 TRANSCRIPT / Source: (synth.) ESCHERICHIA COLI K-12 (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.55 Å3/Da / Density % sol: 56.96 % / Description: NONE
Crystal growpH: 5.6
Details: THE TERNARY COMPLEX ECLEURS-TRNA-AN3017 WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE AT PH 5.6, 14-18 % PEG 6000 AND 200 MM NACL. CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING A CRYOPROTECTING ...Details: THE TERNARY COMPLEX ECLEURS-TRNA-AN3017 WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE AT PH 5.6, 14-18 % PEG 6000 AND 200 MM NACL. CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING A CRYOPROTECTING SOLUTION CONTAINING 22 % ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.2→90.5 Å / Num. obs: 65794 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.99 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.97 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0085refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3N

1h3n


Resolution: 2.2→90.54 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.829 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 3333 5.1 %RANDOM
Rwork0.20682 ---
obs0.20906 62461 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.762 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--0.47 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→90.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6517 1767 3 274 8561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228657
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3612.21712151
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84724.483319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.104151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0351539
X-RAY DIFFRACTIONr_chiral_restr0.110.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215984
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 227 -
Rwork0.261 4578 -
obs--99.77 %
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)
10.08730.00970.05980.2420.02410.2684-0.0167-0.00570.0182-0.0466-0.00080.0125-0.01130.00570.01750.06730.01120.00670.09160.02150.0988-9.583618.666315.2101
20.76620.1882-0.21931.352-0.19560.07920.17810.0604-0.1558-0.117-0.2503-0.1409-0.02930.02210.07220.16610.03850.02010.15540.05930.086210.3273-6.20048.0228
31.3808-0.5109-0.62151.1813-0.05891.05670.09730.1720.1699-0.0489-0.0619-0.2406-0.0669-0.0928-0.03550.01920.03850.04140.13150.03340.165833.858432.151432.8477
42.4943-0.7144-0.09751.2022-0.56271.18790.24030.1873-0.0351-0.3566-0.19770.04640.21010.1712-0.04260.14260.09050.00830.1252-0.0070.02214.1761-31.511917.762
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 - 860

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