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- PDB-7n11: Crystal structure of the M. abscessus LeuRS editing domain in com... -

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Basic information

Entry
Database: PDB / ID: 7n11
TitleCrystal structure of the M. abscessus LeuRS editing domain in complex with epetraborole-AMP adduct
ComponentsLeucine--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / oxaborole / inhibitor / complex / ANTIBIOTIC / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Leucine--tRNA ligase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKalthoff, E. / Schmeing, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Plos Pathog. / Year: 2021
Title: Efficacy of epetraborole against Mycobacterium abscessus is increased with norvaline.
Authors: Sullivan, J.R. / Lupien, A. / Kalthoff, E. / Hamela, C. / Taylor, L. / Munro, K.A. / Schmeing, T.M. / Kremer, L. / Behr, M.A.
History
DepositionMay 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3124
Polymers21,0241
Non-polymers2883
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.249, 51.597, 116.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 21024.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: leuS, D2E76_19720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U0XQP3, leucine-tRNA ligase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 ul of 10 mg/ml protein solution (50 mM Tris pH 7.5, 150 mM NaCl, 2 mM BME) were mixed with 2 ul of crystallization solution (100 mM HEPES pH 7.0, 2.5 M ammonium sulfate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2020
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 25482 / % possible obs: 76.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.84 Å2 / CC1/2: 0.974 / Rpim(I) all: 0.095 / Rrim(I) all: 0.281 / Net I/σ(I): 4.4
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 5.5 % / Num. unique obs: 66 / CC star: 0 / Rpim(I) all: 0.824 / Rrim(I) all: 1.166 / Χ2: 0.077

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000v720data reduction
HKL-2000v720data scaling
PHASER1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AGR

5agr


Resolution: 2.1→38.57 Å / SU ML: 0.2257 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.7031
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 1322 10 %
Rwork0.1841 11898 -
obs0.1882 14741 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 15 131 1594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831492
X-RAY DIFFRACTIONf_angle_d0.99862040
X-RAY DIFFRACTIONf_chiral_restr0.0593226
X-RAY DIFFRACTIONf_plane_restr0.0061272
X-RAY DIFFRACTIONf_dihedral_angle_d23.3975521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.31241420.21531281X-RAY DIFFRACTION95.44
2.18-2.280.26881420.19561278X-RAY DIFFRACTION95.37
2.28-2.40.24621390.18511244X-RAY DIFFRACTION94.27
2.4-2.550.24841410.1861273X-RAY DIFFRACTION93.39
2.55-2.750.20741410.18721273X-RAY DIFFRACTION94.08
2.75-3.030.23931490.18561334X-RAY DIFFRACTION97.69
3.03-3.470.23391510.18081362X-RAY DIFFRACTION99.61
3.47-4.370.191540.15671386X-RAY DIFFRACTION99.74
4.37-38.570.20691630.19691467X-RAY DIFFRACTION98.67

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