[English] 日本語
![](img/lk-miru.gif)
- PDB-2gun: RNA-Binding Affinities and Crystal Structure of Oligonucleotides ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2gun | ||||||
---|---|---|---|---|---|---|---|
Title | RNA-Binding Affinities and Crystal Structure of Oligonucleotides containing Five-Atom Amide-Based Backbone Structures | ||||||
![]() |
| ||||||
![]() | DNA/RNA / DNA:RNA hybrid / amide bearing DNA / thymidine dimers / internucleosidic amide linkage / DNA / RNA / DNA-RNA COMPLEX | ||||||
Function / homology | COBALT (III) ION / SPERMINE / DNA / RNA![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pallan, P.S. / Egli, M. | ||||||
![]() | ![]() Title: RNA-Binding Affinities and Crystal Structure of Oligonucleotides Containing Five-Atom Amide-Based Backbone Structures. Authors: Pallan, P.S. / von Matt, P. / Wilds, C.J. / Altmann, K.-H. / Egli, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 21.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 13.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 417.9 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 2745.793 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
---|---|---|---|---|---|
#2: RNA chain | Mass: 2965.895 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Chemical | #4: Chemical | ChemComp-SPM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.5 mM cobalt hexamine, 5 mM spermine tetrachloride, 80 mM sodium cacodylate buffer (pH = 7.0) and 10% (v/v) 2-methyl-2,4-pentanediol (MPD)., VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 4, 2001 |
Radiation | Monochromator: Si Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9203 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 2602 / Num. obs: 2391 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.057 |
Reflection shell | Highest resolution: 2.8 Å / % possible all: 92.3 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: L. Clowney et.al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases J. Am. Chem. Soc., (1996) 118, 509-518; A. Gelbin et.al., Geometric Parameters in Nucleic ...Stereochemistry target values: L. Clowney et.al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases J. Am. Chem. Soc., (1996) 118, 509-518; A. Gelbin et.al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents J. Am. Chem. Soc., (1996) 118, 519-529. G. Parkinson et. al., New parameters for the refinement of nucleic acid-containing structures Acta Cryst. (1996). D52, 57-64.
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|