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Yorodumi- PDB-1udn: Crystal structure of the tRNA processing enzyme RNase PH from Aqu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1udn | ||||||
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Title | Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus | ||||||
Components | Ribonuclease PH | ||||||
Keywords | TRANSFERASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information tRNA nucleotidyltransferase / tRNA nucleotidyltransferase activity / rRNA catabolic process / tRNA processing / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Ishii, R. / Nureki, O. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus Authors: Ishii, R. / 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 | 1udn.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1udn.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 1udn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1udn ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1udn | HTTPS FTP |
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-Related structure data
Related structure data | 1udoC 1udqC 1udsC 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: 28408.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: RPH / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: O67069, tRNA nucleotidyltransferase | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | #4: 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: 4.43 Å3/Da / Density % sol: 72.25 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ammonium sulfate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: MARRESEARCH / Detector: CCD / Date: Mar 6, 2003 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 23332 / Num. obs: 23052 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.453 / % possible all: 98.9 |
Reflection shell | *PLUS % possible obs: 98.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→41.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2792132.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.5671 Å2 / ksol: 0.341982 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→41.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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