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- PDB-8c8u: Priestia megaterium mupirocin-resistant isoleucyl-tRNA synthetase... -

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Basic information

Entry
Database: PDB / ID: 8c8u
TitlePriestia megaterium mupirocin-resistant isoleucyl-tRNA synthetase 2 complexed with mupirocin
ComponentsIsoleucine--tRNA ligase
KeywordsRNA BINDING PROTEIN / antibiotic / mupirocin-resistant / IleRS2 / RNA-binding / mupirocin
Function / homology
Function and homology information


isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Domain of unknown function (DUF5915) / Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-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 ...Domain of unknown function (DUF5915) / Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MUPIROCIN / L(+)-TARTARIC ACID / Isoleucine--tRNA ligase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsBrkic, A. / Leibundgut, M. / Jablonska, J. / Zanki, V. / Car, Z. / Petrovic Perokovic, V. / Gruic-Sovulj, I. / Ban, N.
Funding support Croatia, Switzerland, European Union, 3items
OrganizationGrant numberCountry
Croatian Science Foundation180567 Croatia
Swiss National Science Foundation180567 Switzerland
European Regional Development FundKK.01.1.1.02.0016European Union
CitationJournal: Nat Commun / Year: 2023
Title: Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif.
Authors: Brkic, A. / Leibundgut, M. / Jablonska, J. / Zanki, V. / Car, Z. / Petrovic Perokovic, V. / Marsavelski, A. / Ban, N. / Gruic-Sovulj, I.
History
DepositionJan 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 27, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoleucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,0927
Polymers117,9221
Non-polymers1,1706
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint0 kcal/mol
Surface area48180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.580, 124.830, 114.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-1701-

HOH

21A-1959-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isoleucine--tRNA ligase / Isoleucyl-tRNA synthetase / IleRS


Mass: 117921.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gram-positive bacterium / Source: (gene. exp.) Priestia megaterium (bacteria) / Strain: DSM-32 / Cell: bacterial / Gene: ileS, BG04_5198 / Variant: de Bary 1884 / Plasmid: pET28b(+) / Details (production host): EMD Biosciences, Cat: 69865-3 / Cell (production host): bacterial / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / Variant (production host): BL21(DE3) / References: UniProt: A0A0B6AVD3, isoleucine-tRNA ligase

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Non-polymers , 5 types, 770 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MRC / MUPIROCIN / 9-[(E)-4-[(2S,3R,4R,5S)-3,4-bis(oxidanyl)-5-[[(2S,3S)-3-[(2S,3S)-3-oxidanylbutan-2-yl]oxiran-2-yl]methyl]oxan-2-yl]-3-methyl-but-2-enoyl]oxynonanoic acid / PSEUDOMONIC ACID


Mass: 500.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H44O9 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.87 %
Description: Single rhombohedral crystals suspended in the solution. Mechanically robust but prone to cracking during temperature change.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1-0.4 M Potassium tartrate 15-25 % (w/v) PEG3350 12.5 mM Hepes-KOH pH=7,5 at 20 oC 25 mM NaCl 5 mM lithium-mupirocin 8.25 mg/ml wt-HVGH-BmIleRS2
PH range: 6.8-8.2
Temp details: Crystal suscteptible to breaking upon temperature change.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999514025591 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 2, 2020 / Details: 2.9 T superbend magnet
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999514025591 Å / Relative weight: 1
ReflectionResolution: 1.901→48.23 Å / Num. obs: 101302 / % possible obs: 90.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 30.49 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.03685 / Rrim(I) all: 0.1352 / Net I/σ(I): 14.93
Reflection shellResolution: 1.901→1.969 Å / Redundancy: 13.4 % / Rmerge(I) obs: 2.579 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 7452 / CC1/2: 0.452 / CC star: 0.789 / Rpim(I) all: 0.7203 / Rrim(I) all: 2.681 / % possible all: 74.27

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20190806data reduction
XSCALE20190806data scaling
PHASERCCP4Interface 7.0.077phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JZS

1jzs


Resolution: 1.901→48.23 Å / SU ML: 0.2232 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 23.1887
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 4034 4.97 %Random selection
Rwork0.1826 77145 --
obs0.1846 81179 93.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.53 Å2
Refinement stepCycle: LAST / Resolution: 1.901→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 73 764 9010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00848493
X-RAY DIFFRACTIONf_angle_d0.909411530
X-RAY DIFFRACTIONf_chiral_restr0.21271262
X-RAY DIFFRACTIONf_plane_restr0.00521488
X-RAY DIFFRACTIONf_dihedral_angle_d14.21323095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.31981300.27992253X-RAY DIFFRACTION79.81
2.02-2.050.34641210.272346X-RAY DIFFRACTION82.76
2.05-2.070.33191300.25542331X-RAY DIFFRACTION83.65
2.07-2.10.28711050.23892422X-RAY DIFFRACTION84.68
2.1-2.130.2721230.22982427X-RAY DIFFRACTION85.8
2.13-2.160.27581350.20962472X-RAY DIFFRACTION87.63
2.16-2.190.26781250.20742500X-RAY DIFFRACTION88.06
2.19-2.230.23471390.2022537X-RAY DIFFRACTION89.17
2.23-2.260.23111310.1992532X-RAY DIFFRACTION90
2.26-2.30.25241290.20392561X-RAY DIFFRACTION90.54
2.3-2.340.21021440.19622587X-RAY DIFFRACTION91.64
2.34-2.390.26541250.19442602X-RAY DIFFRACTION91.3
2.39-2.440.26451390.19162643X-RAY DIFFRACTION93.17
2.44-2.490.23231330.18942685X-RAY DIFFRACTION93.96
2.49-2.550.21651490.19552654X-RAY DIFFRACTION93.78
2.55-2.610.24151340.19012683X-RAY DIFFRACTION94.88
2.61-2.680.23441360.19712685X-RAY DIFFRACTION94.41
2.68-2.760.25821510.19232744X-RAY DIFFRACTION96.5
2.76-2.850.24841580.18452763X-RAY DIFFRACTION96.88
2.85-2.950.22841340.19262790X-RAY DIFFRACTION97.01
2.95-3.070.2291330.20432804X-RAY DIFFRACTION97.83
3.07-3.210.25411640.20442802X-RAY DIFFRACTION98.21
3.21-3.380.22271360.17992836X-RAY DIFFRACTION98.74
3.38-3.590.24161540.18112848X-RAY DIFFRACTION99.14
3.59-3.870.19331590.16552841X-RAY DIFFRACTION98.98
3.87-4.260.19731480.14882909X-RAY DIFFRACTION99.41
4.26-4.880.17781500.14542891X-RAY DIFFRACTION99.67
4.88-6.140.20981560.17552936X-RAY DIFFRACTION99.36
6.14-48.230.1821630.17173061X-RAY DIFFRACTION99.08

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