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Yorodumi- PDB-2cya: Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cya | ||||||
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Title | Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix | ||||||
Components | Tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / TyrRS / Aminoacylation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Kuratani, M. / Sakai, H. / Takahashi, M. / Yanagisawa, T. / Kobayashi, T. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Kuroishi, C. ...Kuratani, M. / Sakai, H. / Takahashi, M. / Yanagisawa, T. / Kobayashi, T. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Kuroishi, C. / Kuramitsu, S. / Terada, T. / Bessho, Y. / Shirouzu, M. / Sekine, S.I. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea Authors: Kuratani, M. / Sakai, H. / Takahashi, M. / Yanagisawa, T. / Kobayashi, T. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Kuroishi, C. / Kuramitsu, S. / Terada, T. / Bessho, Y. / ...Authors: Kuratani, M. / Sakai, H. / Takahashi, M. / Yanagisawa, T. / Kobayashi, T. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Kuroishi, C. / Kuramitsu, S. / Terada, T. / Bessho, Y. / Shirouzu, M. / Sekine, S.I. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cya.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cya.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/2cya ftp://data.pdbj.org/pub/pdb/validation_reports/cy/2cya | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer generated by the crystallographic symmetry. |
-Components
#1: Protein | Mass: 40827.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YA64, tyrosine-tRNA ligase | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, lithium sulfate, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 22, 2004 / Details: MONOCHROMATOR |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 22931 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.036 / Net I/σ(I): 51.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 8.97 / Rsym value: 0.159 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→49.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 505089.2 / Data cutoff low absF: 0 / 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: 44.1793 Å2 / ksol: 0.360964 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→49.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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