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Yorodumi- PDB-1ueu: Divergent evolutions of trinucleotide polymerization revealed by ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ueu | ||||||
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Title | Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure | ||||||
Components | tRNA nucleotidyltransferase | ||||||
Keywords | TRANSFERASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Nureki, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. Authors: Okabe, M. / Tomita, K. / Ishitani, R. / Ishii, R. / Takeuchi, N. / Arisaka, F. / Nureki, O. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ueu.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ueu.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ueu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ueu_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
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Full document | 1ueu_full_validation.pdf.gz | 483.3 KB | Display | |
Data in XML | 1ueu_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1ueu_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/1ueu ftp://data.pdbj.org/pub/pdb/validation_reports/ue/1ueu | HTTPS FTP |
-Related 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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-Components
#1: Protein | Mass: 51469.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: O28126, EC: 2.7.7.25 | ||||
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#2: Chemical | ChemComp-ACT / | ||||
#3: Chemical | #4: Chemical | ChemComp-CTP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG4000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9704 Å |
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Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9704 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.4 Å / Num. obs: 31484 / Biso Wilson estimate: 17.5 Å2 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 90.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 80.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→48.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2010823.54 / 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: 49.1597 Å2 / ksol: 0.336461 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→48.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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