[English] 日本語
![](img/lk-miru.gif)
- PDB-1r3e: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1r3e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit | ||||||
![]() |
| ||||||
![]() | LYASE/RNA / RNA modification / pseudouridylation / LYASE-RNA COMPLEX | ||||||
Function / homology | ![]() tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pan, H. / Agarwalla, S. / Moustakas, D.T. / Finer-Moore, J. / Stroud, R.M. | ||||||
![]() | ![]() Title: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA Recognition Through a Combination of Rigid Docking and Induced Fit Authors: Pan, H. / Agarwalla, S. / Moustakas, D.T. / Finer-Moore, J. / Stroud, R.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 502.2 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: RNA chain | Mass: 5416.227 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
---|---|---|---|---|---|
#2: RNA chain | Mass: 5380.221 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | | Mass: 35516.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulfate, magnesium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.1→15 Å / Num. all: 39270 / Num. obs: 38642 / % possible obs: 98.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 97.5 | |||||||||||||||
Reflection | *PLUS Num. measured all: 525236 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 97.5 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 45.3 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Num. reflection obs: 34732 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |