+
Open data
-
Basic information
Entry | Database: PDB / ID: 231d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF A DNA-PORPHYRIN COMPLEX | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / RIGHT HANDED DNA / DOUBLE HELIX / FLIPPED-OUT BASES / COMPLEXED WITH DRUG | Function / homology | CU(II)MESO(4-N-TETRAMETHYLPYRIDYL)PORPHYRIN / DNA | ![]() Method | ![]() ![]() Lipscomb, L.A. / Zhou, F.X. / Presnell, S.R. / Woo, R.J. / Peek, M.E. / Plaskon, R.R. / Williams, L.D. | ![]() ![]() Title: Structure of DNA-porphyrin complex. Authors: Lipscomb, L.A. / Zhou, F.X. / Presnell, S.R. / Woo, R.J. / Peek, M.E. / Plaskon, R.R. / Williams, L.D. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 14.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 8.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 436.7 KB | Display | |
Data in XML | ![]() | 3 KB | Display | |
Data in CIF | ![]() | 3.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Chemical | ChemComp-PCU / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 296 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. all: 49552 / Num. obs: 1334 |
-
Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→8 Å / σ(F): 1.5
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 1.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.51 Å / Total num. of bins used: 8 / Num. reflection obs: 87 / Rfactor obs: 0.255 |