[English] 日本語
Yorodumi- PDB-182d: DNA-NOGALAMYCIN INTERACTIONS: THE CRYSTAL STRUCTURE OF D(TGATCA) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 182d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | DNA-NOGALAMYCIN INTERACTIONS: THE CRYSTAL STRUCTURE OF D(TGATCA) COMPLEXED WITH NOGALAMYCIN | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | NOGALAMYCIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | Authors | Smith, C.K. / Davies, G.J. / Dodson, E.J. / Moore, M.H. | Citation | Journal: Biochemistry / Year: 1995 | Title: DNA-nogalamycin interactions: the crystal structure of d(TGATCA) complexed with nogalamycin. Authors: Smith, C.K. / Davies, G.J. / Dodson, E.J. / Moore, M.H. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 182d.cif.gz | 24 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb182d.ent.gz | 14.8 KB | Display | PDB format |
PDBx/mmJSON format | 182d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 182d_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 182d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 182d_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 182d_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/82/182d ftp://data.pdbj.org/pub/pdb/validation_reports/82/182d | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 1808.229 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 |
Detector | Type: HENDRIX-LENTFER / Detector: IMAGE PLATE |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. obs: 4953 / Observed criterion σ(I): 3 |
Reflection | *PLUS Highest resolution: 1.8 Å / % possible obs: 81 % / Observed criterion σ(I): 3 / Num. measured all: 4788 / Rmerge(I) obs: 0.057 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→10 Å / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 1 / Rfactor obs: 0.195 / Rfactor Rfree: 0.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30 Å2 |