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Yorodumi- PDB-2e3c: Crystal structure of the catalytic domain of pyrrolysyl-tRNA synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e3c | ||||||
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Title | Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase | ||||||
Components | Pyrrolysyl-tRNA synthetasePyrrolysine—tRNAPyl ligase | ||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / tRNA / pyrrolysine / translation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Yanagisawa, T. / Ishii, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase Authors: Yanagisawa, T. / Ishii, R. / Fukunaga, R. / Kobayashi, T. / Sakamoto, K. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e3c.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e3c.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 2e3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/2e3c ftp://data.pdbj.org/pub/pdb/validation_reports/e3/2e3c | HTTPS FTP |
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-Related structure data
Related structure data | 2zceC 2dxh 2dxg 2dz8 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33344.164 Da / Num. of mol.: 1 / Fragment: C-terminal catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: JCM9314 / Gene: pylS / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase |
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#2: Water | ChemComp-HOH / |
Sequence details | THIS CONFLICT IS DUE TO THE STRAIN DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Na/Cacodylate, MgCl2, PEG3350, pH 7, 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: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. obs: 12559 / % possible obs: 91.9 % / Biso Wilson estimate: 45.6 Å2 |
Reflection shell | Resolution: 2.64→2.67 Å / % possible all: 67.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DXH 2dxh Resolution: 2.65→38.1 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1388388.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.4333 Å2 / ksol: 0.29724 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→38.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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