[English] 日本語
Yorodumi- PDB-1idw: STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1idw | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF RH(NH3)6+++ | ||||||||||||||||||
Components | 5'-R(*Keywords | DNA/RNA / RNA/DNA HYBRID / RHODIUM HEXAMMINE / C-U MISMATCH / G-U MISMATCH / DNA-RNA COMPLEX | Function / homology | RHODIUM HEXAMINE ION / DNA/RNA hybrid | Function and homology information Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å | Authors | Cruse, W. / Saludjian, P. / Neuman, A. / Prange, T. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues Authors: Cruse, W. / Saludjian, P. / Neuman, A. / Prange, T. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Structure of a Mispaired RNA Double Helix at 1.6 A Resolution and Implications for the Prediction of RNA Secondary Structure Authors: Cruse, W. / Saludjian, P. / Biala, E. / Strazewski, P. / Prange, T. / Kennard, O. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1idw.cif.gz | 22.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1idw.ent.gz | 14.1 KB | Display | PDB format |
PDBx/mmJSON format | 1idw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1idw_validation.pdf.gz | 342 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1idw_full_validation.pdf.gz | 353.6 KB | Display | |
Data in XML | 1idw_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1idw_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1idw ftp://data.pdbj.org/pub/pdb/validation_reports/id/1idw | HTTPS FTP |
-Related structure data
Related structure data | 1icgC 1id9C 1ihaC 165dS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The second strand of the dimer is not symmetric |
-Components
#1: DNA/RNA hybrid | Mass: 2843.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phosphoramidite method #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.66 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: cacodylate buffer, MPD, Rhodium-hexammine, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 20, 1997 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→6 Å / Num. all: 3738 / Num. obs: 3641 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.041 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.8→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3 / Num. unique all: 517 / Rsym value: 0.206 / % possible all: 43.2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 6 Å / % possible obs: 85 % / Num. measured all: 13027 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 165D Resolution: 1.8→6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 Stereochemistry target values: personal dictionary from small molecules Details: Chloro-uracil 9 B disordered at the C2 position. Refined as two-component 1:1 static orientations paired to their symmetry-related mates. The two rhodium atoms are refined anisotropically. ...Details: Chloro-uracil 9 B disordered at the C2 position. Refined as two-component 1:1 static orientations paired to their symmetry-related mates. The two rhodium atoms are refined anisotropically. One chlorine atom is disordered.
| ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|