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- PDB-1ivs: CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE C... -
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Open data
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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 | ||||||
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![]() | LIGASE/RNA / Rossmann fold / helix bundle / coiled coil / beta barrel / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / LIGASE-RNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fukai, S. / Nureki, O. / Sekine, S.-I. / Shimada, A. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 441.4 KB | Display | ![]() |
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PDB format | ![]() | 352.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 565.9 KB | Display | ![]() |
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Full document | ![]() | 707.9 KB | Display | |
Data in XML | ![]() | 55.6 KB | Display | |
Data in CIF | ![]() | 83.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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