[English] 日本語

- PDB-1vec: Crystal structure of the N-terminal domain of rck/p54, a human DE... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1vec | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein | ||||||
![]() | ATP-dependent RNA helicase p54 | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() mRNA decay by 5' to 3' exoribonuclease / miRNA-mediated gene silencing by inhibition of translation / viral RNA genome packaging / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hogetsu, K. / Matsui, T. / Yukihiro, Y. / Tanaka, M. / Sato, T. / Kumasaka, T. / Tanaka, N. | ||||||
![]() | ![]() Title: Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes Authors: Matsui, T. / Hogetsu, K. / Usukura, J. / Sato, T. / Kumasaka, T. / Akao, Y. / Tanaka, N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 95 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 77.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 252.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 262 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qdeS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23113.076 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / | #3: Chemical | ChemComp-TLA / | ![]() #4: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG3350, di-sodium tartrate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 15, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.01→29.9 Å / Num. all: 52406 / Num. obs: 52054 / % possible obs: 99.3 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.01→2.08 Å / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5271 / % possible all: 98.2 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1QDE Resolution: 2.01→29.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 116477.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4738 Å2 / ksol: 0.335418 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→29.9 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|