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- PDB-1yfr: crystal structure of alanyl-tRNA synthetase in complex with ATP a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yfr | ||||||
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Title | crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium | ||||||
![]() | Alanyl-tRNA synthetase | ||||||
![]() | LIGASE / alpha-beta fold / bent ATP conformation / magnesium bridge | ||||||
Function / homology | ![]() alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Swairjo, M.A. / Schimmel, P.R. | ||||||
![]() | ![]() Title: Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. Authors: Swairjo, M.A. / Schimmel, P.R. #1: ![]() Title: Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition. Authors: Swairjo, M.A. / Otero, F.J. / Yang, X.-L. / Lovato, M.A. / Skene, R.J. / McRee, D.E. / Ribas de Pouplana, L. / Schimmel, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.4 KB | Display | ![]() |
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PDB format | ![]() | 154.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1yfsC ![]() 1yftC ![]() 1ygbC ![]() 1riqS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53772.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.2 Details: PEG 5000 monomethyl ether, NaCl, Tris-Cl, Tris-base, ATP, MgCl2, pH 6.2, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2004 / Details: curved crystal |
Radiation | Monochromator: curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97976 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 50235 / Num. obs: 50235 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.25 / Num. unique all: 5064 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1RIQ Resolution: 2.15→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→50 Å
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Refine LS restraints |
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