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Yorodumi- PDB-1yfs: The crystal structure of alanyl-tRNA synthetase in complex with L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yfs | ||||||
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Title | The crystal structure of alanyl-tRNA synthetase in complex with L-alanine | ||||||
Components | Alanyl-tRNA synthetaseAlanine—tRNA ligase | ||||||
Keywords | LIGASE / alpha-beta fold / helix-loop-helix motif / amino acid binding | ||||||
Function / homology | Function and homology information alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / negative regulation of DNA-templated transcription / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Swairjo, M.A. / Schimmel, P.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 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: Journal: Mol.Cell / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yfs.cif.gz | 194.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yfs.ent.gz | 154.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yfs ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yfs | HTTPS FTP |
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-Related structure data
Related structure data | 1yfrC 1yftC 1ygbC 1riqS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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Details | The assymetric unit contains two biological units. The biological unit is the complex of one alanyl-tRNA synthetase molecule with one L-alanine molecule. |
-Components
#1: Protein | Mass: 53772.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: alaS / Plasmid: PET20B+ / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O67323, alanine-tRNA ligase #2: Chemical | #3: 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 | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: PEG 5000 mme, NaCl, Tris-Cl, Tris-base, L-alanine, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 57744 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RIQ Resolution: 2.08→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: 22.6 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→50 Å
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