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

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Basic information

Entry
Database: PDB / ID: 5ags
TitleCrystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex with the adduct 3-(Aminomethyl)-4-bromo-7-ethoxybenzo[c][1,2]oxaborol-1(3H)-ol-AMP
ComponentsLEUCYL-TRNA SYNTHETASE
KeywordsLIGASE / M.TUBERCULOSIS / LEUCINE-TRNA LIGASE ACTIVITY / 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 editing 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-38Y / METHIONINE / Leucine--tRNA ligase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 9, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
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: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6553
Polymers24,8911
Non-polymers7642
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.750, 62.160, 76.990
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 /


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 K-12 (bacteria) / Variant (production host): DE3 RIL / References: UniProt: P9WFV1, leucine-tRNA ligase
#2: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-38Y / 3-(AMINOMETHYL)-4-BROMO-7-ETHOXYBENZO[C][1,2]OXABOROL-1(3H)-OL-MODIFIED ADENOSINE


Mass: 615.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25BBrN6O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 42.9 % / 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: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.47→38.7 Å / Num. obs: 35180 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4

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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: 1.47→38.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.133 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 1857 5 %RANDOM
Rwork0.18339 ---
obs0.18459 35180 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.287 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.47→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 46 277 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221623
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9922236
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.58922.70374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82815237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0571517
X-RAY DIFFRACTIONr_chiral_restr0.1590.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211285
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_it0.6751.51005
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20721613
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7453618
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7224.5613
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: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 141 -
Rwork0.262 2520 -
obs--98.41 %

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