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- PDB-8c9d: Priestia megaterium W130Q mutant of type 2 isoleucyl-tRNA synthet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c9d | ||||||||||||
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Title | Priestia megaterium W130Q mutant of type 2 isoleucyl-tRNA synthetase complexed with an isoleucyl-adenylate analogue | ||||||||||||
![]() | Isoleucine--tRNA ligase | ||||||||||||
![]() | RNA BINDING PROTEIN / antibiotic / mupirocin-resistant / IleRS2 / RNA-binding protein / C-terminal domain | ||||||||||||
Function / homology | ![]() 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 | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Brkic, A. / Leibundgut, M. / Jablonska, J. / Zanki, V. / Car, Z. / Petrovic Perokovic, V. / Ban, N. / Gruic-Sovulj, I. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.3 KB | Display | ![]() |
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PDB format | ![]() | 180 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8c8uC ![]() 8c8vC ![]() 8c8wC ![]() 8c9eC ![]() 8c9fC ![]() 8c9gC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 117863.875 Da / Num. of mol.: 1 / Mutation: W130Q Source method: isolated from a genetically manipulated source Details: Gram-positive bacterium / Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.81 % Description: Single rhombohedral crystals suspended in the solution. Mechanically robust but prone to cracking during 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 W130Q-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 ...Details: 5 mM Ile-AMS and 16.5 mg/ml W130Q-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: 6.8-8.2 Temp details: Crystal suscteptible to breaking upon temperature change. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 17, 2021 / Details: 2.9 T superbend magnet |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99986928994751 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.34 Å / Num. obs: 64242 / % possible obs: 93.27 % / Redundancy: 25.6 % / Biso Wilson estimate: 43.62 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1511 / Rpim(I) all: 0.0301 / Rrim(I) all: 0.1541 / Net I/σ(I): 22.62 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 21 % / Rmerge(I) obs: 2.203 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 5093 / CC1/2: 0.531 / CC star: 0.833 / Rpim(I) all: 0.0301 / Rrim(I) all: 2.395 / % possible all: 81 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 58.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.34 Å
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Refine LS restraints |
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LS refinement shell |
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