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Yorodumi- PDB-1is1: Crystal structure of ribosome recycling factor from Vibrio paraha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1is1 | ||||||
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Title | Crystal structure of ribosome recycling factor from Vibrio parahaemolyticus | ||||||
Components | RIBOSOME RECYCLING FACTOR | ||||||
Keywords | TRANSLATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nakano, H. / Yamaichi, Y. / Uchiyama, S. / Yoshida, T. / Nishina, K. / Kato, H. / Ohkubo, T. / Honda, T. / Yamagata, Y. / Kobayashi, Y. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium Authors: Nakano, H. / Yoshida, T. / Uchiyama, S. / Kawachi, M. / Matsuo, H. / Kato, T. / Ohshima, A. / Yamaichi, Y. / Honda, T. / Kato, H. / Yamagata, Y. / Ohkubo, T. / Kobayashi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1is1.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1is1.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 1is1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/1is1 ftp://data.pdbj.org/pub/pdb/validation_reports/is/1is1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20635.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GRF5 |
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#2: 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: 2.39 Å3/Da / Density % sol: 48.58 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 8000, sodium acetate, GDP, fusidic acid, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 10326 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 2.2→2.24 Å / % possible all: 93.7 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 82069 |
Reflection shell | *PLUS Rmerge(I) obs: 0.251 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refinement | *PLUS Highest resolution: 2.2 Å / Num. reflection obs: 9947 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.207 |