[English] 日本語
![](img/lk-miru.gif)
- PDB-2nlm: Crystal structure of the DB 911- D(CGCGAATTCGCG)2 complex at 2.05... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2nlm | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the DB 911- D(CGCGAATTCGCG)2 complex at 2.05 A resolution. | ||||||||||||||||||
![]() | 5'-D(*![]() ![]() Function / homology | Chem-DB9 / | ![]() ![]() Method | ![]() ![]() ![]() Lee, M.P.H. / Neidle, S. | ![]() ![]() Title: Crystal structure of the DB 911 - D(CGCGAATTCGCG)2 complex at 2.05 A resolution. Authors: Lee, M.P.H. / Neidle, S. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 25.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 15.6 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 |
-
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-DB9 / | #4: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.07 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MAGNESIUM CHLORIDE, DNA DODECAMER, MPD, COMPOUND DB 911, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING 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: Jul 31, 2006 / 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: 2.05→20.03 Å / Num. obs: 4291 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 3.36 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 5 / % possible all: 98.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE. Resolution: 2.05→8 Å / Num. parameters: 2239 / Num. restraintsaints: 2544 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||
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: 559 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→8 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|