+
Open data
-
Basic information
Entry | Database: PDB / ID: 1m69 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Atomic Resolution Structure of 5Br-9amino-DACA with d[CGTACG]2 | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / atomic resolution / adenine-thymine disorder / topoisomerase II poison | Function / homology | Chem-DAX / SPERMINE / DNA | ![]() Method | ![]() ![]() ![]() ![]() Teixeira, S.C.M. / Thorpe, J.H. / Todd, A.K. / Cardin, C.J. | ![]() ![]() Title: Heavy Going: the Atomic Resolution Structure of a Topoisomerase II Poison Intercalating into DNA in Multiple Orientations Also Reveals a Multiple Adenine-Thymine Hydrogen Bonding Pattern Authors: Teixeira, S.C.M. / Thorpe, J.H. / Todd, A.K. / Cardin, C.J. #1: ![]() Title: Reading University: Single Crystal X-Ray Diffraction Studies of DNA and DNA-drug complexes Authors: Todd, A.K. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 28.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 20.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 55.21 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Ammonium acetate, magnesium acetate, sodium cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290.15K | ||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 10, 2001 |
Radiation | Monochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8068 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→10 Å / Num. obs: 8308 / % possible obs: 94.72 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.1→1.15 Å / % possible all: 95.79 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: ddf073 structure, with corrected sequence Resolution: 1.1→10 Å / Num. parameters: 2113 / Num. restraintsaints: 3689 / Cross valid method: FREE R / σ(F): 4 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 81 / Occupancy sum non hydrogen: 190.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.1→1.15 Å /
|