[English] 日本語
![](img/lk-miru.gif)
- PDB-1y7f: Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1y7f | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy(methyleneamino)oxy]ethyl] Thymidine (T*) | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / A-DNA / modified | Function / homology | : / DNA | ![]() Method | ![]() ![]() ![]() Egli, M. / Minasov, G. / Tereshko, V. / Pallan, P.S. / Teplova, M. / Inamati, G.B. / Lesnik, E.A. / Owens, S.R. / Ross, B.S. / Prakash, T.P. / Manoharan, M. | ![]() ![]() Title: Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of ...Title: Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications. Authors: Egli, M. / Minasov, G. / Tereshko, V. / Pallan, P.S. / Teplova, M. / Inamati, G.B. / Lesnik, E.A. / Owens, S.R. / Ross, B.S. / Prakash, T.P. / Manoharan, M. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 24.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 15.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 378.6 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wv5C ![]() 1wv6C ![]() 1y84C ![]() 1y86C ![]() 1y8lC ![]() 1y8vC ![]() 1y9fC ![]() 1y9sC ![]() 1yb9C ![]() 1ybcC ![]() 410dS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | Chains A and B form duplex |
-
Components
#1: DNA chain | Mass: 3150.098 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-BA / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.31 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 20mM Na-Cacodilate, 2mM Spermine, 5mM Barium Chloride, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 13, 1998 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 6913 / Num. obs: 6913 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.4 / Num. unique all: 627 / % possible all: 90.3 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 410D Resolution: 1.6→17 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: Conjugate gradient refinement using maximum likelihood target for amplitudes
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→17 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.64 Å
|