[English] 日本語
![](img/lk-miru.gif)
- PDB-1qde: CRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TRANSLATION INITIATION ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1qde | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TRANSLATION INITIATION FACTOR 4A FROM SACCHAROMYCES CEREVISIAE-THE PROTOTYPE OF THE DEAD BOX PROTEIN FAMILY | ||||||
![]() | TRANSLATION INITIATION FACTOR 4A | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / ATP-dependent activity, acting on RNA / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / ATP-dependent activity, acting on RNA / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Benz, J. / Trachsel, H. / Baumann, U. | ||||||
![]() | ![]() Title: Crystal structure of the ATPase domain of translation initiation factor 4A from Saccharomyces cerevisiae--the prototype of the DEAD box protein family. Authors: Benz, J. / Trachsel, H. / Baumann, U. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25165.982 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 9-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: PQE30 / Production host: ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-SO4 / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.62 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: PEG 8000, MGCL2, (NH4)2SO4, MES, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→40 Å / Num. all: 14988 / Num. obs: 14988 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.07 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.315 / % possible all: 99.1 |
Reflection | *PLUS Rmerge(I) obs: 0.09 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |