[English] 日本語
![](img/lk-miru.gif)
- PDB-1vbx: Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme P... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1vbx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in EDTA solution | ||||||
![]() |
| ||||||
![]() | TRANSLATION/RNA / HDV / ![]() ![]() | ||||||
Function / homology | ![]() U1 snRNP binding / U1 snRNP / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ke, A. / Zhou, K. / Ding, F. / Cate, J.H.D. / Doudna, J.A. | ||||||
![]() | ![]() Title: A Conformational Switch controls hepatitis delta virus ribozyme catalysis Authors: Ke, A. / Zhou, K. / Ding, F. / Cate, J.H.D. / Doudna, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 72.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1sj3C ![]() 1sj4C ![]() 1sjfC ![]() 1vbyC ![]() 1vbzC ![]() 1vc0C ![]() 1vc5C ![]() 1vc6C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: RNA chain | ![]() Mass: 24467.521 Da / Num. of mol.: 1 / Mutation: C75U / Source method: obtained synthetically Details: RNA occurs from Hapatitis Delta Virus pathogen, in vitro transcription with pUc19 |
---|---|
#2: Protein | Mass: 11498.472 Da / Num. of mol.: 1 / Fragment: U1A_RBD(residues 1-100) / Mutation: Y31H/Q36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.4 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: NaCl, EDTA, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→35.23 Å / Num. all: 12113 / Num. obs: 11760 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Biso Wilson estimate: 33.9 Å2 |
Reflection shell | Resolution: 2.7→2.87 Å / % possible all: 93.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.3069 Å2 / ksol: 0.324505 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.7 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→35.23 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|