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- PDB-8c9g: Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase... -

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Basic information

Entry
Database: PDB / ID: 8c9g
TitlePriestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase 1 complexed with mupirocin
ComponentsIsoleucine--tRNA ligase
KeywordsRNA BINDING PROTEIN / antibiotic / mupirocin-sensitive / IleRS1
Function / homology
Function and homology information


isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Isoleucine-tRNA ligase, type 1 / Isoleucyl tRNA synthetase type 1, anticodon-binding domain / Isoleucine-tRNA ligase / Zinc finger, FPG/IleRS-type / Zinc finger found in FPG and IleRS / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase ...Isoleucine-tRNA ligase, type 1 / Isoleucyl tRNA synthetase type 1, anticodon-binding domain / Isoleucine-tRNA ligase / Zinc finger, FPG/IleRS-type / Zinc finger found in FPG and IleRS / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / 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
Similarity search - Domain/homology
MUPIROCIN / Isoleucine--tRNA ligase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBrkic, A. / Leibundgut, M. / Jablonska, J. / Zanki, V. / Car, Z. / Petrovic Perokovic, V. / Ban, N. / Gruic-Sovulj, I.
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 22, 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
B: Isoleucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,70815
Polymers210,1812
Non-polymers1,52713
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, Mupirocin is known to bind close homologs of the studied enzymes.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Isoleucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7516
Polymers105,0911
Non-polymers6605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.820, 144.280, 108.370
Angle α, β, γ (deg.)90.000, 95.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 105090.719 Da / Num. of mol.: 2
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_1180 / 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: A0A0B6A6A8, isoleucine-tRNA ligase

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Non-polymers , 6 types, 39 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.: 2 / Source method: obtained synthetically / Formula: C26H44O9 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Description: Plate clusters. Pieces can be broken of the cluster for freezing and diffraction experiments.
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Solution of 20 mg/ml wt-HMGH-PmIleRS1 with added 3 mM mupirocin was mixed in 1:1 ratio with the well solution containing: 400 - 900 mM LiCl and 10 - 20% PEG3350, 25 mM Hepes-KOH pH=7.5 at 20 ...Details: Solution of 20 mg/ml wt-HMGH-PmIleRS1 with added 3 mM mupirocin was mixed in 1:1 ratio with the well solution containing: 400 - 900 mM LiCl and 10 - 20% PEG3350, 25 mM Hepes-KOH pH=7.5 at 20 oC, 50 mM NaCl. The drop volume of 2 microliters, was equilibrated towards 300 microliters of the well solution at 19 degrees.
PH range: 6.8-7.5 / Temp details: Crystals do not grow at 4 degrees.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999873570222 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999873570222 Å / Relative weight: 1
ReflectionResolution: 2.8→60.39 Å / Num. obs: 49643 / % possible obs: 90.26 % / Redundancy: 3.6 % / Biso Wilson estimate: 57.17 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.09249 / Rrim(I) all: 0.1767 / Net I/σ(I): 6.95
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3810 / CC1/2: 0.373 / Rpim(I) all: 0.7865 / Rrim(I) all: 1.513 / % possible all: 75.64

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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 / Resolution: 2.8→60.39 Å / SU ML: 0.3967 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 27.9342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.258 1812 3.99 %
Rwork0.1995 43602 -
obs0.2018 45414 90.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→60.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14802 0 91 26 14919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215274
X-RAY DIFFRACTIONf_angle_d0.452820717
X-RAY DIFFRACTIONf_chiral_restr0.03962250
X-RAY DIFFRACTIONf_plane_restr0.00332673
X-RAY DIFFRACTIONf_dihedral_angle_d11.75875741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.34741140.3062787X-RAY DIFFRACTION75.53
2.88-2.960.37021270.29442906X-RAY DIFFRACTION78.58
2.96-3.060.37891240.29273041X-RAY DIFFRACTION81.91
3.06-3.170.34591330.27453126X-RAY DIFFRACTION84.1
3.17-3.290.31691320.25583237X-RAY DIFFRACTION87.92
3.29-3.440.31321390.23883349X-RAY DIFFRACTION90.72
3.44-3.620.27681420.21323442X-RAY DIFFRACTION92.51
3.62-3.850.26561400.19523493X-RAY DIFFRACTION94.09
3.85-4.150.24761510.18883591X-RAY DIFFRACTION96.87
4.15-4.560.22161530.15993631X-RAY DIFFRACTION97.75
4.56-5.220.21881510.16653659X-RAY DIFFRACTION98.35
5.23-6.580.25071530.20853655X-RAY DIFFRACTION97.62
6.58-60.390.20331530.15633685X-RAY DIFFRACTION97.29

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