[English] 日本語
Yorodumi- PDB-2yy3: Crystal Structure of translation elongation factor EF-1 beta from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yy3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of translation elongation factor EF-1 beta from Pyrococcus horikoshii | ||||||
Components | Elongation factor 1-beta | ||||||
Keywords | TRANSLATION / Elongation factor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Ishii, T. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of translation elongation factor EF-1 beta from Pyrococcus horikoshii Authors: Ishii, T. / Bessho, Y. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yy3.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yy3.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 2yy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yy3_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2yy3_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 2yy3_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 2yy3_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yy3 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yy3 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10457.496 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P58748 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.36 % / Description: the file contains Friedel pairs. |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.1M Tris-HCl, 0.2M Lithium Sulfate, 2M Ammonium Sulfate, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.97874, 0.97904, 0.99476 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 8, 2007 | ||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 32040 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.051 | ||||||||||||
Reflection shell | Resolution: 2.5→2.6 Å / Rsym value: 0.299 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.5→32.18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 330020.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.0065 Å2 / ksol: 0.347946 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→32.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|