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Yorodumi- PDB-8c9e: Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c9e | ||||||||||||
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Title | Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase 1 complexed with an isoleucyl-adenylate analogue | ||||||||||||
Components | Isoleucine--tRNA ligase | ||||||||||||
Keywords | RNA 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 / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Priestia megaterium (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 8c9e.cif.gz | 469 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c9e.ent.gz | 325.7 KB | Display | PDB format |
PDBx/mmJSON format | 8c9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/8c9e ftp://data.pdbj.org/pub/pdb/validation_reports/c9/8c9e | HTTPS FTP |
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-Related structure data
Related structure data | 8c8uC 8c8vC 8c8wC 8c9dC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 105090.719 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_1180 / Plasmid: pET28b(+) / Details (production host): Kan(R) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B6A6A8, isoleucine-tRNA ligase |
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-Non-polymers , 6 types, 18 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-LI / | #7: Chemical | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66.03 % Description: Single bipyramidal 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 20 mg/ml wt-HMGH-PmIleRS1 were mixed in 1:1 ratio with the well solution containing: 300 mM lithium sulfate, 150 mM sodium sulfate, and 15 - 25 % PEG3350, 25 mM Hepes-KOH ...Details: 5 mM Ile-AMS and 20 mg/ml wt-HMGH-PmIleRS1 were mixed in 1:1 ratio with the well solution containing: 300 mM lithium sulfate, 150 mM sodium sulfate, and 15 - 25 % 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: 6.8-8.2 Temp details: Susceptible 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: X06SA / Wavelength: 1.0000305674359 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0000305674359 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.77 Å / Num. obs: 34322 / % possible obs: 92.86 % / Redundancy: 20.8 % / Biso Wilson estimate: 110.52 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06695 / Rpim(I) all: 0.01511 / Rrim(I) all: 0.06867 / Net I/σ(I): 30.66 |
Reflection shell | Resolution: 2.9→3.004 Å / Redundancy: 22 % / Rmerge(I) obs: 3.219 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2499 / CC1/2: 0.605 / CC star: 0.868 / Rpim(I) all: 0.7003 / Rrim(I) all: 3.295 / % possible all: 74.11 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.77 Å / SU ML: 0.488 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 33.4581 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: 155.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→48.77 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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