[English] 日本語
![](img/lk-miru.gif)
- PDB-8ec1: 5'-CGCGAATTCGCG-3' and benzimidazole diamidine (DB1476) comlpex w... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8ec1 | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 5'-CGCGAATTCGCG-3' and benzimidazole diamidine (DB1476) comlpex with ligand orientation I | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / MINOR GROOVE / SMALL MOLECULE | Function / homology | Chem-WFB / DNA / DNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() Ogbonna, E.N. / Wilson, W.D. | Funding support | | ![]()
![]() ![]() Title: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences. Authors: Ogbonna, E.N. / Paul, A. / Farahat, A.A. / Terrell, J.R. / Mineva, E. / Ogbonna, V. / Boykin, D.W. / Wilson, W.D. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 35.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 589.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 589.3 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ed6C ![]() 8edaC ![]() 8edbC ![]() 8f1sC ![]() 8f1vC ![]() 8f20C ![]() 8f2wC ![]() 8f2yC ![]() 8f94C ![]() 8fb4C ![]() 8fdpC ![]() 8fdqC ![]() 8fdrC ![]() 1bnaS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Label seq-ID: 1 - 12
|
-
Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: A self-complementary DNA (5'-CGCGAATTCGCG-3') bound by ligand (DB1476) in a type I orientation. Source: (synth.) ![]() #2: Chemical | ChemComp-WFB / | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: magnesium chloride hexahydrate, sodium chloride, potassium chloride, double-stranded DNA, MPD ,spermine tetrahydrate, sodium cacodylate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2022 Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror water |
Radiation | Monochromator: double crystal - water cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→34.2 Å / Num. obs: 8886 / % possible obs: 99 % / Redundancy: 1.2 % / CC1/2: 1 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.63→1.69 Å / Num. unique obs: 807 / CC1/2: 1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1BNA Resolution: 1.63→34.19 Å / SU B: 25.89 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 0.19 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.89 Å2 / Biso mean: 28 Å2 / Biso min: 16.63 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.63→34.19 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 14.7949 Å / Origin y: 20.9234 Å / Origin z: 9.0799 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|