[English] 日本語
![](img/lk-miru.gif)
- PDB-1i7j: CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.19 A RE... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1i7j | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.19 A RESOLUTION. 2-METHYL-2,4-PENTANEDIOL AND MAGNESIUM BINDING. | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / 2'-O-MeRNA duplex / 2-methyl-2 / 4-pentanediol / magnesium / groove hydration and binding | Function / homology | RNA | ![]() Method | ![]() ![]() ![]() ![]() Adamiak, D.A. / Rypniewski, W.R. / Milecki, J. / Adamiak, R.W. | ![]() ![]() Title: The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove. Authors: Adamiak, D.A. / Rypniewski, W.R. / Milecki, J. / Adamiak, R.W. #1: ![]() Title: CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.3 A RESOLUTION. HYDRATION PATTERN OF 2'-O-METHYLATED RNA Authors: Adamiak, D.A. / Milecki, J. / Popenda, W. / Adamiak, R.W. / Dauter, A. / Rypniewski, W.R. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 32.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 25.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 390.1 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Data in CIF | ![]() | 5.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 310dS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: RNA chain | Mass: 1990.361 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15 mM MgCl2, 1 mM spermine tetrahydrochloride and 30-40% 2-methyl-2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 1996 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→20 Å / Num. obs: 8715 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.19→1.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / Num. unique all: 415 / % possible all: 94 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 8715 / Num. measured all: 150605 |
Reflection shell | *PLUS % possible obs: 94 % |
-
Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB 310D Resolution: 1.19→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CCP4
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.19→20 Å
| ||||||||||||||||
Refine LS restraints |
| ||||||||||||||||
LS refinement shell | Resolution: 1.19→1.21 Å /
| ||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |