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Yorodumi- PDB-8c8v: Priestia megaterium mupirocin-resistant isoleucyl-tRNA synthetase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c8v | ||||||||||||
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Title | Priestia megaterium mupirocin-resistant isoleucyl-tRNA synthetase 2 with a fully-resolved C-terminal tRNA-binding domain complexed with an isoleucyl-adenylate analogue | ||||||||||||
Components | Isoleucine--tRNA ligase | ||||||||||||
Keywords | RNA BINDING PROTEIN / antibiotic / mupirocin-resistant / IleRS2 / RNA-binding protein / C-terminal domain | ||||||||||||
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 / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Brkic, A. / Leibundgut, M. / Jablonska, J. / Zanki, V. / Car, Z. / Petrovic Perokovic, V. / Ban, N. / Gruic-Sovulj, I. | ||||||||||||
Funding support | Croatia, Switzerland, European Union, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c8v.cif.gz | 286.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c8v.ent.gz | 182.6 KB | Display | PDB format |
PDBx/mmJSON format | 8c8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/8c8v ftp://data.pdbj.org/pub/pdb/validation_reports/c8/8c8v | HTTPS FTP |
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-Related structure data
Related structure data | 8c8uC 8c8wC 8c9dC 8c9eC 8c9fC 8c9gC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 NBRC 15308 = ATCC 14581 (bacteria) Strain: DSM-32 / Cell: bacterial / Gene: ileS, BG04_5198 / Variant: (de Bary 1884) Gupta et al. 2020 / 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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#2: Chemical | #3: Chemical | ChemComp-ILA / | #4: Chemical | ChemComp-TAR / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.7 % Description: Single tetragonal crystals. Susceptible to cracking upon temperature change. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5 mM Ile-AMS and 16.5 mg/ml wt-HVGH-PmIleRS2 were mixed in 1:1 ratio with the well solution containing: 0.2-0.5 M Potassium tartrate, 10-20 % (w/v) PEG3350, 25 mM Hepes-KOH pH=7,5 at 20 oC, ...Details: 5 mM Ile-AMS and 16.5 mg/ml wt-HVGH-PmIleRS2 were mixed in 1:1 ratio with the well solution containing: 0.2-0.5 M Potassium tartrate, 10-20 % (w/v) 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 4 degrees. PH range: 6.8-8.1 Temp details: Crystals are prone to cracking upon temperature change. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2022 / Details: 17 T superbend magnet |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.31 Å / Num. obs: 72948 / % possible obs: 94.1 % / Redundancy: 12.7 % / Biso Wilson estimate: 42.13 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07646 / Rpim(I) all: 0.02219 / Rrim(I) all: 0.07967 / Net I/σ(I): 26.51 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 5848 / CC1/2: 0.62 / CC star: 0.875 / Rpim(I) all: 0.4262 / Rrim(I) all: 1.388 / % possible all: 81.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.31 Å / SU ML: 0.2595 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 23.4279 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.31 Å
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Refine LS restraints |
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LS refinement shell |
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