[English] 日本語
Yorodumi- PDB-1ik5: Crystal Structure of a 14mer RNA Containing Double UU Bulges in T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ik5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a 14mer RNA Containing Double UU Bulges in Two Crystal Forms: A Novel U*(AU) Intramolecular Base Triple | ||||||
Components |
| ||||||
Keywords | RNA / RNA duplex / UU-bulges / base triple / kink | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Deng, J. / Xiong, Y. / Sudarsanakumar, C. / Shi, K. / Sundaralingam, M. | ||||||
Citation | Journal: RNA / Year: 2001 Title: Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple. Authors: Deng, J. / Xiong, Y. / Sudarsanakumar, C. / Shi, K. / Sundaralingam, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ik5.cif.gz | 26.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ik5.ent.gz | 18 KB | Display | PDB format |
PDBx/mmJSON format | 1ik5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ik5_validation.pdf.gz | 390.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ik5_full_validation.pdf.gz | 390.6 KB | Display | |
Data in XML | 1ik5_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1ik5_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/1ik5 ftp://data.pdbj.org/pub/pdb/validation_reports/ik/1ik5 | HTTPS FTP |
-Related structure data
Related structure data | 1fufC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 4503.547 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: potential hair pin fragment with highly conserved UUCG loop | ||
---|---|---|---|
#2: RNA chain | Mass: 4504.531 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: cacodylate, magnesium chloride, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 140 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 2, 2000 |
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 | *PLUS Highest resolution: 1.8 Å / Num. obs: 7100 / % possible obs: 91 % / Rmerge(I) obs: 0.06 |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→10 Å / σ(F): 2
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.209 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|