[English] 日本語
Yorodumi- PDB-161d: A SINGLE 2'-HYDROXYL GROUP CONVERTS B-DNA TO A-DNA: CRYSTAL STRUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 161d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | A SINGLE 2'-HYDROXYL GROUP CONVERTS B-DNA TO A-DNA: CRYSTAL STRUCTURE OF THE DNA-RNA CHIMERIC DECAMER DUPLEX D(CCGGC)R(G)D(CCGG) WITH A NOVEL INTERMOLECULAR G.C BASE-PAIRED QUADRUPLET | ||||||||||||||||||
Components | DNA/RNA (5'-D(*Keywords | DNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX | Function / homology | DNA/RNA hybrid | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | Authors | Ban, C. / Ramakrishnan, B. / Sundaralingam, M. | Citation | Journal: J.Mol.Biol. / Year: 1994 | Title: A single 2'-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d(CCGGC)r(G)d(CCGG) with a novel intermolecular G-C base-paired quadruplet. Authors: Ban, C. / Ramakrishnan, B. / Sundaralingam, M. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 161d.cif.gz | 20.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb161d.ent.gz | 13.4 KB | Display | PDB format |
PDBx/mmJSON format | 161d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 161d_validation.pdf.gz | 348 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 161d_full_validation.pdf.gz | 353.8 KB | Display | |
Data in XML | 161d_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 161d_validation.cif.gz | 3.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/61/161d ftp://data.pdbj.org/pub/pdb/validation_reports/61/161d | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA/RNA hybrid | Mass: 3062.980 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: 2.36 Å3/Da / Density % sol: 47.87 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE |
Detector | Type: SIEMENS-NICOLET / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å / Num. all: 8769 / Num. obs: 2837 / Observed criterion σ(I): 1 |
Reflection | *PLUS Rmerge(I) obs: 0.021 |
-Processing
Software | Name: X-PLOR / Classification: refinement | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→8 Å / σ(F): 1 /
| |||||||||||||||
Refine Biso |
| |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
| |||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 2753 / σ(F): 1 / Rfactor obs: 136 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
|