[English] 日本語
![](img/lk-miru.gif)
- PDB-8taj: Sequence specific (AATT) orientation of netropsin molecules at a ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8taj | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Sequence specific (AATT) orientation of netropsin molecules at a unique minor groove binding site (position1) within a self-assembled 3D DNA lattice (4x6) | ||||||||||||
![]() |
| ||||||||||||
![]() | DNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice / Minor Groove Binders / Netropsin / DAPI / Hoechst / ImPyPy / polyamide / host-guest | ||||||||||||
Function / homology | CACODYLATE ION / NETROPSIN / DNA / DNA (> 10)![]() | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Simmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals. Authors: Simmons, C.R. / Buchberger, A. / Henry, S.J.W. / Novacek, A. / Fahmi, N.E. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 36.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 22.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 626.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 628.1 KB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t7bC ![]() 8t7xC ![]() 8t80C ![]() 8ta8C ![]() 8ta9C ![]() 8tamC ![]() 8tapC ![]() 8taqC ![]() 8tb3C ![]() 8tb4C ![]() 8tb8C ![]() 8tbdC ![]() 8tboC ![]() 8tc2C ![]() 8tc4C ![]() 8tc6C ![]() 8tdtC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-DNA chain , 4 types, 4 molecules ABCD
#1: DNA chain | Mass: 6456.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 1769.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 2432.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2137.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/CAC.gif)
![](data/chem/img/NT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NT.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CAC / |
---|---|
#6: Chemical | ChemComp-NT / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 6.07 Å3/Da / Density % sol: 79.75 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5 mL of 0.05 M Na Cacodylate pH 6.5 with 30 mM MgCl2, 1.0 mM spermine, and 1.3 M Li2SO4 was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock. Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 6234 / % possible obs: 93.3 % / Redundancy: 9.9 % / CC1/2: 0.976 / CC star: 0.994 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.037 / Rrim(I) all: 0.12 / Χ2: 3.32 / Net I/σ(I): 5.7 / Num. measured all: 61699 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→34.109 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell |
|