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Yorodumi- PDB-1ivs: CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ivs | ||||||
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Title | CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE | ||||||
Components |
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Keywords | LIGASE/RNA / Rossmann fold / helix bundle / coiled coil / beta barrel / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / LIGASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information valine-tRNA ligase / valine-tRNA ligase activity / valyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å | ||||||
Authors | Fukai, S. / Nureki, O. / Sekine, S.-I. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: RNA / Year: 2003 Title: Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase Authors: Fukai, S. / Nureki, O. / Sekine, S.-I. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S. #1: Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: STRUCTURAL BASIS FOR DOUBLE-SIEVE DISCRIMINATION OF L-VALINE FROM L-ISOLEUCINE AND L-THREONINE BY THE COMPLEX OF TRNA(VAL) AND VALYL-TRNA SYNTHETASE Authors: Fukai, S. / Nureki, O. / Sekine, S. / Shimada, A. / Tao, J. / Vassylyev, D.G. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ivs.cif.gz | 441.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ivs.ent.gz | 352.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ivs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ivs_validation.pdf.gz | 565.9 KB | Display | wwPDB validaton report |
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Full document | 1ivs_full_validation.pdf.gz | 707.9 KB | Display | |
Data in XML | 1ivs_validation.xml.gz | 55.6 KB | Display | |
Data in CIF | 1ivs_validation.cif.gz | 83.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1ivs ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1ivs | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 24174.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: tRNA (Val) with the CAC anticodon #2: Protein | Mass: 98914.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: valS / Plasmid: pK7 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P96142, valine-tRNA ligase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium Sulfate, Magnesium Sulfate, Cacodylate Na, 1,8-diaminooctane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃Details: Fukai, S., (2000) Cell (Cambridge,Mass.), 103, 793. | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 24, 1998 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 150310 / Num. obs: 150310 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 56.5 Å2 |
Reflection shell | Resolution: 2.9→3.08 Å / % possible all: 87.9 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.9→40 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.6469 Å2 / ksol: 0.297208 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.247 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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