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- PDB-1nyr: Structure of Staphylococcus aureus threonyl-tRNA synthetase compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nyr | ||||||
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Title | Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP | ||||||
![]() | threonyl-tRNA synthetase 1 | ||||||
![]() | LIGASE / threonyl-tRNA synthetase / ATP / threonine | ||||||
Function / homology | ![]() threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / transferase activity / tRNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Torres-Larios, A. / Sankaranarayanan, R. / Rees, B. / Dock-Bregeon, A.C. / Moras, D. | ||||||
![]() | ![]() Title: Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase Authors: Torres-Larios, A. / Sankaranarayanan, R. / Rees, B. / Dock-Bregeon, A.C. / Moras, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 274.6 KB | Display | ![]() |
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PDB format | ![]() | 219.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 60.8 KB | Display | |
Data in CIF | ![]() | 82.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nyqC ![]() 1qf6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The protein is a homodimer made of chains A and B |
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Components
#1: Protein | Mass: 74562.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 60.89 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, Tris.Cl, potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 / 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 22, 1999 / Details: mirrors |
Radiation | Monochromator: 2 Silicon crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25 Å / Num. all: 46973 / Num. obs: 46973 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 79.9 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2998 / % possible all: 95.7 |
Reflection | *PLUS Num. measured all: 160435 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / % possible obs: 95.7 % / Num. unique obs: 2998 / Rmerge(I) obs: 0.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1QF6 Resolution: 2.8→15 Å / Rfactor Rfree error: 0.007 / 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: 58.1117 Å2 / ksol: 0.334807 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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