[English] 日本語
Yorodumi- PDB-165d: THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 165d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE | ||||||||||||||||||
Components | DNA/RNA (5'-R(*Keywords | DNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX / OVERHANGING BASES / MODIFIED / MISMATCHED | Function / homology | RHODIUM HEXAMINE ION / RNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å | Authors | Cruse, W. / Saludjian, P. / Biala, E. / Strazewski, P. / Prange, T. / Kennard, O. | Citation | 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.B. / Saludjian, P. / Biala, E. / Strazewski, P. / Prange, T. / Kennard, O. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 165d.cif.gz | 21.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb165d.ent.gz | 14.3 KB | Display | PDB format |
PDBx/mmJSON format | 165d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/65/165d ftp://data.pdbj.org/pub/pdb/validation_reports/65/165d | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: THE DEOXY-BROMO-URACIL +U IS WELL ORDERED ON STRAND A BUT NOT ON STRAND B (RESIDUE +U 18) WHERE TWO (50:50) DISORDERED POSITIONS WERE GIVEN. FOUR RHODIUM HEXAMINE IONS RH(NH3)6 ++ WERE LOCATED ...1: THE DEOXY-BROMO-URACIL +U IS WELL ORDERED ON STRAND A BUT NOT ON STRAND B (RESIDUE +U 18) WHERE TWO (50:50) DISORDERED POSITIONS WERE GIVEN. FOUR RHODIUM HEXAMINE IONS RH(NH3)6 ++ WERE LOCATED (NAMED RHD), TWO WITH FULL OCCUPANCY FACTORS (RESIDUES 19 AND 20) AND TWO WITH PARTIAL OCCUPANCIES (RESIDUES 21 AND 22). | ||||||||
Components on special symmetry positions |
|
-Components
#1: RNA chain | Mass: 2887.600 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-RHD / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.26 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: pH 6.30, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.3 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||
Detector |
| ||||||||||||
Radiation |
| ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Highest resolution: 1.6 Å / Num. obs: 6093 / Observed criterion σ(F): 2 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.6 Å |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.55→10 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|