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Yorodumi- PDB-1ek8: CRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR (RRF) FROM ESC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ek8 | ||||||
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Title | CRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR (RRF) FROM ESCHERICHIA COLI | ||||||
Components | RIBOSOME RECYCLING FACTOR | ||||||
Keywords | TRANSLATION / ribosome / translation factor / t-RNA mimicry / coiled coil | ||||||
Function / homology | Function and homology information cytoplasmic translational termination / ribosomal large subunit binding / translation / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Min, K. / Suh, S.W. / Kim, K.K. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Crystal structure of the ribosome recycling factor from Escherichia coli. Authors: Kim, K.K. / Min, K. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ek8.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ek8.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ek8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ek8 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ek8 | 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
#1: Protein | Mass: 20671.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P0A805 | ||||
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#2: Chemical | #3: Chemical | ChemComp-DEM / | #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: 2.29 Å3/Da / Density % sol: 46.38 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES-NaOH, 10 % PEG 350 MME, 12 % PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 53.4 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 14 ℃ | |||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 1.0074 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0074 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 29485 / Num. obs: 8691 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.34 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.23 / Num. unique all: 858 / % possible all: 97.7 |
Reflection | *PLUS Num. measured all: 29485 |
Reflection shell | *PLUS % possible obs: 97.7 % / Num. unique obs: 858 / Rmerge(I) obs: 0.23 |
-Processing
Software |
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Refinement | Resolution: 2.3→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.228 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 53.9 Å2 |