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- PDB-5agr: Crystal structure of the LeuRS editing domain of Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 5agr
TitleCrystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex with the adduct (S)-3-(Aminomethyl)-7-ethoxybenzo[c][1,2]oxaborol-1(3H)-ol-AMP
ComponentsLEUCINE--TRNA LIGASE
KeywordsLIGASE / ATP + L-LEUCINE + TRNA(LEU) GIVES AMP + DIPHOSPHATE + L-LEUCYL- TRNA(LEU) AMINOACYL-TRNA EDITING ACTIVITY / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / NOVEL BORON INHIBITORS OF LEURS
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / peptidoglycan-based cell wall / ATP binding / plasma membrane / cytosol
Similarity search - Function
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 / 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) ...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 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-A52 / LEUCINE / METHIONINE / Leucine--tRNA ligase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPalencia, A. / Li, X. / Alley, M.R.K. / Ding, C. / Easom, E.E. / Hernandez, V. / Meewan, M. / Mohan, M. / Rock, F.L. / Franzblau, S.G. ...Palencia, A. / Li, X. / Alley, M.R.K. / Ding, C. / Easom, E.E. / Hernandez, V. / Meewan, M. / Mohan, M. / Rock, F.L. / Franzblau, S.G. / Wang, Y. / Lenaerts, A.J. / Parish, T. / Cooper, C.B. / Waters, M.G. / Ma, Z. / Mendoza, A. / Barros, D. / Cusack, S. / Plattner, J.J.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2016
Title: Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium Tuberculosis that Target Leucyl-tRNA Synthetase.
Authors: Palencia, A. / Li, X. / Bu, W. / Choi, W. / Ding, C.Z. / Easom, E.E. / Feng, L. / Hernandez, V. / Houston, P. / Liu, L. / Meewan, M. / Mohan, M. / Rock, F.L. / Sexton, H. / Zhang, S. / Zhou, ...Authors: Palencia, A. / Li, X. / Bu, W. / Choi, W. / Ding, C.Z. / Easom, E.E. / Feng, L. / Hernandez, V. / Houston, P. / Liu, L. / Meewan, M. / Mohan, M. / Rock, F.L. / Sexton, H. / Zhang, S. / Zhou, Y. / Wan, B. / Wang, Y. / Franzblau, S.G. / Woolhiser, L. / Gruppo, V. / Lenaerts, A.J. / O'Malley, T. / Parish, T. / Cooper, C.B. / Waters, M.G. / Ma, Z. / Ioerger, T.R. / Sacchettini, J.C. / Rullas, J. / Angulo-Barturen, I. / Perez-Herran, E. / Mendoza, A. / Barros, D. / Cusack, S. / Plattner, J.J. / Alley, M.R.K.
History
DepositionFeb 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.4Jan 10, 2024Group: 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 / 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 / _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

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Assembly

Deposited unit
A: LEUCINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7665
Polymers24,8911
Non-polymers8764
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.330, 61.850, 77.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LEUCINE--TRNA LIGASE / LEUCYL-TRNA SYNTHETASE / LEURS / LEUCYL-TRNA SYNTHETASE


Mass: 24890.756 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN (CP1), RESIDUES 309-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P9WFV1, leucine-tRNA ligase

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Non-polymers , 5 types, 271 molecules

#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-A52 / 3-AMINOMETHYL-7-(ETHOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine


Mass: 533.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23BN6O9P
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCONTAINS A N-TERM SEQUENCE BELONGING TO PETM-11 EMBL VECTOR

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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: 2.1 Å3/Da / Density % sol: 42.1 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M BIS-TRIS PH 5.5, 17% W/V PEG 10000, 0.2 M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.3→35.5 Å / Num. obs: 48494 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 4 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AJG

2ajg


Resolution: 1.3→38.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.673 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19657 2668 5.2 %RANDOM
Rwork0.16915 ---
obs0.17059 48494 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.222 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 57 267 1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221591
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9942187
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7165211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8622.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35115229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3371517
X-RAY DIFFRACTIONr_chiral_restr0.1470.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211244
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_it0.8451.5987
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47521578
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1043604
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2034.5597
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.9431591
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 213 -
Rwork0.239 3603 -
obs--98.94 %

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