[English] 日本語
Yorodumi- PDB-1y8v: Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y8v | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thymidine (T*) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / A-DNA / O2'-modification / decamer | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | 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. | Citation | Journal: Biochemistry / Year: 2005 | 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1y8v.cif.gz | 23.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1y8v.ent.gz | 15.2 KB | Display | PDB format |
PDBx/mmJSON format | 1y8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y8v_validation.pdf.gz | 375.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1y8v_full_validation.pdf.gz | 375.1 KB | Display | |
Data in XML | 1y8v_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 1y8v_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y8v ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y8v | HTTPS FTP |
-Related structure data
Related structure data | 1wv5C 1wv6C 1y7fC 1y84C 1y86C 1y8lC 1y9fC 1y9sC 1yb9C 1ybcC 410dS C: citing same article (ref.) 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: 3103.085 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.6 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM KCL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 10, 1998 / Details: Mirrors |
Radiation | Monochromator: No / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 8698 / Num. obs: 8698 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.4 / Num. unique all: 820 / % possible all: 97.4 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 410D Resolution: 1.5→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 Details: Conjugate gradient refinement using maximum likelihood target for amplitudes
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.53 Å
|