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- PDB-7n12: Crystal structure of the M. abscessus LeuRS editing domain in com... -

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Basic information

Entry
Database: PDB / ID: 7n12
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
Chem-365 / Leucine--tRNA ligase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
B: Leucine--tRNA ligase
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2755
Polymers42,0492
Non-polymers1,2273
Water6,918384
1
B: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6863
Polymers21,0241
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5902
Polymers21,0241
Non-polymers5651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.439, 37.107, 100.287
Angle α, β, γ (deg.)90.000, 112.279, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-726-

HOH

21A-716-

HOH

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Components

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


Mass: 21024.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: leuS, D2E76_19720 / Plasmid: pMabsED / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0U0XQP3, leucine-tRNA ligase
#2: Chemical ChemComp-365 / [(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl dihydrogen phosphate / 3-AMINOMETHYL-7-(3-HYDROXY-PROPOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine


Mass: 565.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27BN6O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 ul 7.5 mg/ml protein solution (50 mM Tris pH 7.5, 150 mM NaCl. 2 mM BME) was mixed with crystallization solution (100 mM HEPES, pH 7.5, 2% PEG400, 2.1 M ammonium sulfate, 10 mM AMP, 1 mM ...Details: 2 ul 7.5 mg/ml protein solution (50 mM Tris pH 7.5, 150 mM NaCl. 2 mM BME) was mixed with crystallization solution (100 mM HEPES, pH 7.5, 2% PEG400, 2.1 M ammonium sulfate, 10 mM AMP, 1 mM epetraborole, 15% glycerol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.52131 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52131 Å / Relative weight: 1
ReflectionResolution: 1.52→92.97 Å / Num. obs: 56594 / % possible obs: 94.21 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.5 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.11 / Rsym value: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 5.35 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2931 / CC1/2: 0.833 / Rpim(I) all: 0.214 / Rrim(I) all: 0.506 / % possible all: 99.57

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALS3.4.3data reduction
DIALS3.4.3data scaling
PHASER1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AGR

5agr


Resolution: 1.7→92.8 Å / SU ML: 0.2045 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 20.9308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 4142 5.01 %Random selection
Rwork0.184 78589 --
obs0.1861 56594 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.84 Å2
Refinement stepCycle: LAST / Resolution: 1.7→92.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 5 384 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01282936
X-RAY DIFFRACTIONf_angle_d1.21614035
X-RAY DIFFRACTIONf_chiral_restr0.0686454
X-RAY DIFFRACTIONf_plane_restr0.0088523
X-RAY DIFFRACTIONf_dihedral_angle_d21.34471057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.33191260.29972575X-RAY DIFFRACTION99.52
1.72-1.740.27621130.2782660X-RAY DIFFRACTION99.28
1.74-1.760.29931590.25082669X-RAY DIFFRACTION99.16
1.76-1.780.2961450.24342564X-RAY DIFFRACTION98.9
1.78-1.810.28581270.23352595X-RAY DIFFRACTION99.2
1.81-1.830.26231370.22422612X-RAY DIFFRACTION98.92
1.83-1.860.26111400.21372686X-RAY DIFFRACTION99.3
1.86-1.890.30021500.21832531X-RAY DIFFRACTION99.3
1.89-1.910.24231410.20452578X-RAY DIFFRACTION99.45
1.91-1.950.24041490.20092671X-RAY DIFFRACTION99.09
1.95-1.980.22541280.18352614X-RAY DIFFRACTION99.06
1.98-2.020.24481590.18612530X-RAY DIFFRACTION98.03
2.02-2.050.2061360.17092676X-RAY DIFFRACTION98.7
2.05-2.10.25511360.17812580X-RAY DIFFRACTION99.85
2.1-2.140.21381440.17812664X-RAY DIFFRACTION99.57
2.14-2.190.20731200.16672645X-RAY DIFFRACTION99.86
2.19-2.250.2331290.17452567X-RAY DIFFRACTION99.89
2.25-2.310.25391480.17322673X-RAY DIFFRACTION99.72
2.31-2.380.22211410.16432609X-RAY DIFFRACTION99.75
2.38-2.450.21581500.17682613X-RAY DIFFRACTION99.64
2.45-2.540.19081410.1692601X-RAY DIFFRACTION99.67
2.54-2.640.22981450.17192659X-RAY DIFFRACTION99.47
2.64-2.760.2241280.17482624X-RAY DIFFRACTION99.85
2.76-2.910.20861530.1842610X-RAY DIFFRACTION99.86
2.91-3.090.21911160.17452662X-RAY DIFFRACTION98.86
3.09-3.330.211670.17232629X-RAY DIFFRACTION99.93
3.33-3.660.19371490.15732563X-RAY DIFFRACTION99.2
3.66-4.190.23291190.16622647X-RAY DIFFRACTION99.03
4.19-5.280.18931120.17062644X-RAY DIFFRACTION99.67
5.28-92.80.23691340.22942638X-RAY DIFFRACTION99.78

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