[English] 日本語
Yorodumi- PDB-375d: A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 375d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / UNUSUAL DNA/RNA / DOUBLE HELIX / DOUBLE DRUG IN MINOR GROOVE / COMPLEXED WITH DRUG / MISMATCHED | Function / homology | NETROPSIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | Authors | Chen, X. / Rao, S.T. / Sekar, K. / Sundaralingam, M. | Citation | Journal: Nucleic Acids Res. / Year: 1998 | Title: A Novel End-to-End Binding of Two Netropsins to the DNA Decamers d(CCCCCIIIII) 2, d(CCCBr5CCIIIII)2, d(CBr5CCCCIIIII)2 Authors: Chen, X. / Mitra, S.N. / Rao, S.T. / Sekar, K. / Sundaralingam, M. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 375d.cif.gz | 29.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb375d.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 375d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 375d_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 375d_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 375d_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 375d_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/75/375d ftp://data.pdbj.org/pub/pdb/validation_reports/75/375d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 2971.911 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | ChemComp-NT / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 291 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. obs: 8546 / % possible obs: 73 % / Observed criterion σ(I): 1.4 / Redundancy: 1.98 % / Rmerge(I) obs: 0.045 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→8 Å / σ(F): 4
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|