+Open data
-Basic information
Entry | Database: PDB / ID: 1eh1 | ||||||
---|---|---|---|---|---|---|---|
Title | RIBOSOME RECYCLING FACTOR FROM THERMUS THERMOPHILUS | ||||||
Components | RIBOSOME RECYCLING FACTOR | ||||||
Keywords | RIBOSOME / TRANSLATION / HINGE VARIABILITY | ||||||
Function / homology | Function and homology information cytoplasmic translational termination / ribosomal large subunit binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.6 Å | ||||||
Authors | Toyoda, T. / Tin, O.F. / Ito, K. / Fujiwara, T. / Kumasaka, T. / Yamamoto, M. / Garber, M.B. / Nakamura, Y. | ||||||
Citation | Journal: RNA / Year: 2000 Title: Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch. Authors: Toyoda, T. / Tin, O.F. / Ito, K. / Fujiwara, T. / Kumasaka, T. / Yamamoto, M. / Garber, M.B. / Nakamura, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1eh1.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1eh1.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 1eh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eh1_validation.pdf.gz | 409.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1eh1_full_validation.pdf.gz | 415.4 KB | Display | |
Data in XML | 1eh1_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1eh1_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1eh1 ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1eh1 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21029.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WX76 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.9 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: ammonium sulphate, sodium acetate, MES, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 30, 1999 / Details: GRAPHITE CRYSTAL |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 7568 / Num. obs: 28513 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.234 / Num. unique all: 7568 / % possible all: 98.7 |
Reflection | *PLUS Num. obs: 7568 / Num. measured all: 28513 |
Reflection shell | *PLUS % possible obs: 98.7 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.6→10 Å / Data cutoff low absF: 0 / σ(F): 2 / σ(I): 3 Stereochemistry target values: RAMACHANDRAN ET AL BBA 359:298 (1974)
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.02 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 5.42 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.1 |