[English] 日本語
Yorodumi- PDB-1d88: CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d88 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL STRUCTURES OF DNA-RNA CHIMERIC DUPLEXES | ||||||||||||||||||
Components | DNA/RNA (5'-D(*Keywords | DNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX / DNA-RNA HYBRID COMPLEX | Function / homology | DNA/RNA hybrid | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Egli, M. / Usman, N. / Rich, A. | Citation | Journal: Biochemistry / Year: 1993 Title: Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes. Authors: Egli, M. / Usman, N. / Rich, A. #1: Journal: Nucleic Acids Res. / Year: 1992 Title: Large Scale Chemical Synthesis, Purification and Crystallization of RNA-DNA Chimeras Authors: Usman, N. / Egli, M. / Rich, A. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Crystal Structure of an Okazaki Fragment at 2 Angstroms Resolution Authors: Egli, M. / Usman, N. / Zhang, S. / Rich, A. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1d88.cif.gz | 25 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1d88.ent.gz | 14.6 KB | Display | PDB format |
PDBx/mmJSON format | 1d88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d88_validation.pdf.gz | 323.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1d88_full_validation.pdf.gz | 345.6 KB | Display | |
Data in XML | 1d88_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 1d88_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/1d88 ftp://data.pdbj.org/pub/pdb/validation_reports/d8/1d88 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA/RNA hybrid | Mass: 3061.004 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 291.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6 / Details: Egli, M., (1992) Proc.Nat.Acad.Sci.USA, 89, 534. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 273 K |
---|---|
Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 2285 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 2 Å / Rmerge F obs: 2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Highest resolution: 2 Å / σ(F): 2 /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Num. reflection obs: 2285 / σ(F): 2 / Rfactor obs: 0.195 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |