+
Open data
-
Basic information
Entry | Database: PDB / ID: 8edb | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 5'-CGCGAATTCGCG-3' and an AT-specific binder (DB1884) complex | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / SMALL MOLECULE / MINOR GROOVE | Function / homology | 4,4'-(1H-indole-2,6-diyl)dibenzenecarboximidamide / 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 | ![]() | 35.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 22.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 388.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 388.5 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ec1C ![]() 8ed6C ![]() 8edaC ![]() 8f1sC ![]() 8f1vC ![]() 8f20C ![]() 8f2wC ![]() 8f2yC ![]() 8f94C ![]() 8fb4C ![]() 8fdpC ![]() 8fdqC ![]() 8fdrC 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 the ligand DB1884. Source: (synth.) ![]() #2: Chemical | ChemComp-884 / | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRAHYDROCHLORIDE, POTASSIUM CHLORIDE, MAGNESIUM CHLORIDE HEXAHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25.24 Å / Num. obs: 10249 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.99 / Net I/σ(I): 17.92 |
Reflection shell | Resolution: 1.55→1.6 Å / Num. unique obs: 1004 / CC1/2: 0.99 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: IBNA Resolution: 1.55→25.24 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.71 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.08 Å2 / Biso mean: 24.2403 Å2 / Biso min: 12.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→25.24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
|