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Yorodumi- PDB-2cyc: Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cyc | ||||||
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Title | Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Pyrococcus horikoshii | ||||||
Components | tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / Tyrosine / 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 | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kuratani, M. / Sakai, H. / Takahashi, M. / Yanagisawa, T. / Kobayashi, T. / Sakamoto, K. / Terada, T. / Shirouzu, M. / Sekine, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 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. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cyc.cif.gz | 171.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cyc.ent.gz | 136.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/2cyc ftp://data.pdbj.org/pub/pdb/validation_reports/cy/2cyc | 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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-Components
#1: Protein | Mass: 43342.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58739, tyrosine-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: 3.26 Å3/Da / Density % sol: 62.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: PEG20000, Tyrosine, Magnesium Chloride, Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2005 / 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: 53700 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.051 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 6.76 / Rsym value: 0.214 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2706341.06 / 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: 57.67 Å2 / ksol: 0.385334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→37.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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