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Yorodumi- PDB-1ffy: INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ffy | ||||||
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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 / STAPHYLOCOCCUS AUREUS / PROTEIN-RNA COMPLEX / METAL IONS / EDITING TRNA SYNTHETASE / DOUBLE-SIEVE / MUPIROCIN / 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 / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ffy.cif.gz | 250.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ffy.ent.gz | 191.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ffy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ffy_validation.pdf.gz | 466.3 KB | Display | wwPDB validaton report |
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Full document | 1ffy_full_validation.pdf.gz | 521.7 KB | Display | |
Data in XML | 1ffy_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 1ffy_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/1ffy ftp://data.pdbj.org/pub/pdb/validation_reports/ff/1ffy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain / Protein , 2 types, 2 molecules TA
#1: RNA chain | Mass: 24236.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IN VITRO TRANSCRIPTION OF E.COLI tRNA SEQUENCE |
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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 |
-Non-polymers , 5 types, 342 molecules
#3: Chemical | ChemComp-K / | ||||||
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#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-MRC / | #7: 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: 2.55 Å3/Da / Density % sol: 51.82 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: PEG 6000, SODIUM CACODYLATE, MgCl2, MGSO4, KCL, ZnCl2, BETA OCTYL GLUCOPYRANOSIDE, BETA MERCAPTOETHANOL, BICINE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 Details: This particular structure is not described in this paper. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.94 |
Detector | Type: PRINCETON 2K / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→500 Å / Num. obs: 67758 / % possible obs: 89.1 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.079 |
-Processing
Software |
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Refinement | Resolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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