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- PDB-8c9g: Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c9g | ||||||||||||
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Title | Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase 1 complexed with mupirocin | ||||||||||||
![]() | Isoleucine--tRNA ligase | ||||||||||||
![]() | RNA BINDING PROTEIN / antibiotic / mupirocin-sensitive / IleRS1 | ||||||||||||
Function / homology | ![]() 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 | ||||||||||||
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 | ![]() | 466.6 KB | Display | ![]() |
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PDB format | ![]() | 302.9 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 ![]() 8c9dC ![]() 8c9eC ![]() 8c9fC 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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2 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 105090.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Gram-positive bacterium / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 39 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MRC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MRC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.27 % Description: Plate clusters. Pieces can be broken of the cluster for freezing and diffraction experiments. |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999873570222 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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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: 64.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→60.39 Å
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Refine LS restraints |
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LS refinement shell |
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