+
Open data
-
Basic information
Entry | Database: PDB / ID: 2b3e | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of DB819-D(CGCGAATTCGCG)2 complex. | ||||||||||||||||||
![]() | 5'-D(*![]() ![]() ![]() ![]() ![]() Function / homology | Chem-DBN / | ![]() ![]() Method | ![]() ![]() ![]() Campbell, N.H. / Evans, D.A. / Lee, M.P. / Parkinson, G.N. / Neidle, S. | ![]() ![]() Title: Targeting the DNA minor groove with fused ring dicationic compounds: Comparison of in silico screening and a high-resolution crystal structure. Authors: Campbell, N.H. / Evans, D.A. / Lee, M.P. / Parkinson, G.N. / Neidle, S. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 28.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 17.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2dbeS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: AT-RICH REGION IN THE GENOME OF ORGANISMS. #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-DBN / | #4: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.64 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 293 K / pH: 7 Details: MAGNESIUM CHLORIDE, DNA, COMPOUND DB819, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.00 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 23, 2005 / Details: OSMIC FOCUSING MIRROR SYSTEM |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.36→25 Å / Num. obs: 13180 / % possible obs: 92.2 % / Observed criterion σ(I): -2 / Redundancy: 4.38 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 56.82 |
Reflection shell | Resolution: 1.36→1.41 Å / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.03 / % possible all: 60.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE Resolution: 1.36→8 Å / Num. parameters: 2511 / Num. restraintsaints: 2558 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 624 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→8 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|