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Yorodumi- PDB-1qu3: INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qu3 | ||||||
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Title | INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH TRNA(ILE) AND MUPIROCIN | ||||||
Components |
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Keywords | LIGASE/RNA / SHUTTLING MECHANISM / EDITING TRNA SYNTHETASE / DOUBLE-SIEVE / METAL IONS / HYDROLYTIC FUNCTION / LIGASE-RNA COMPLEX | ||||||
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 | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | ||||||
Authors | Silvian, L.F. / Wang, J. / Steitz, T.A. | ||||||
Citation | Journal: Science / Year: 1999 Title: Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Authors: Silvian, L.F. / Wang, J. / Steitz, T.A. #1: Journal: To be Published Title: Metal Ions that Stabilize the tRNA and Mediate the Recognition by its Cognate Synthetase Authors: Wang, J. / Silvian, L.F. / Steitz, T.A. #2: Journal: To be Published Title: Switching from a Resting to Synthetic and Hydrolytic Modes in Editing tRNA Synthetases Authors: Wang, J. / Silvian, L.F. / Steitz, T.A. #3: Journal: To be Published Title: Structure Based Drug Design Against Mupirocin Resistant Staphylococcus Aureus Authors: Wang, J. / Silvian, L.F. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qu3.cif.gz | 237.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qu3.ent.gz | 181.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/1qu3 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/1qu3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 24236.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 105057.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P41972, isoleucine-tRNA ligase |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-MRC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: evaporation / Details: EVAPORATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.009 |
Detector | Type: PRINCETON 2K / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→100 Å / Num. all: 23256 / Num. obs: 23256 / % possible obs: 89.5 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.099 |
Reflection | *PLUS Rmerge(I) obs: 0.099 |
-Processing
Refinement | Resolution: 2.9→10 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 375201.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.25 Å2 / ksol: 0.312 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 4.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.394 / % reflection Rfree: 5.7 % / Rfactor Rwork: 0.36 |