[English] 日本語
![](img/lk-miru.gif)
- PDB-1yrm: Crystal Structure of an RNA duplex containing site specific 2'-am... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1yrm | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a C-A mismatch | ||||||||||||||||||
![]() | DNA/RNA (5'-R(*![]() RNA / 2'-AMINE / DUPLEX / MISMATCH | Function / homology | STRONTIUM ION / DNA/RNA hybrid / DNA/RNA hybrid (> 10) | ![]() Method | ![]() ![]() ![]() Gherghe, C.M. / Krahn, J.M. / Weeks, K.M. | ![]() ![]() Title: Crystal structures, reactivity and inferred acylation transition States for 2'-amine substituted RNA. Authors: Gherghe, C.M. / Krahn, J.M. / Weeks, K.M. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 37.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 25.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 387.1 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yy0C ![]() 1yzdC ![]() 1z79C ![]() 1z7fC C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: DNA/RNA hybrid | Mass: 5081.094 Da / Num. of mol.: 3 / Source method: obtained synthetically #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.65 % | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8 Details: MPD, cacodylate, spermidine, strontium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K | ||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→21.5 Å / Num. all: 5573 / Num. obs: 5305 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 13.09 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.041 / Net I/σ(I): 17.19 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.77 / Num. unique all: 395 / Rsym value: 0.187 / % possible all: 75.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: NDB ENTRY AR0002 Resolution: 2.5→7.98 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 696091 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.6756 Å2 / ksol: 0.228829 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7.98 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|