[English] 日本語
Yorodumi- PDB-304d: SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICATATIC) IN TH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 304d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICATATIC) IN THE MONOCLINIC FORM | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / DOUBLE DRUG IN THE MINOR GROOVE | Function / homology | DISTAMYCIN A / DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | Authors | Chen, X. / Ramakrishnan, B. / Sundaralingam, M. | Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC). Authors: Chen, X. / Ramakrishnan, B. / Sundaralingam, M. #1: Journal: Nat.Struct.Biol. / Year: 1994 Title: Binding of two Distamycin A Molecules in the Minor Groove of an Alternating B-DNA Authors: Chen, X. / Ramakrishnan, B. / Rao, S.T. / Sundaralingam, M. #2: Journal: Nat.Struct.Biol. / Year: 1995 Title: Crystal Structures of B-Form DNA-RNA Chimers Complexed with Distamycin Authors: Chen, X. / Ramakrishnan, B. / Sundaralingam, M. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 304d.cif.gz | 15.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb304d.ent.gz | 9.1 KB | Display | PDB format |
PDBx/mmJSON format | 304d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/04/304d ftp://data.pdbj.org/pub/pdb/validation_reports/04/304d | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 2396.589 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Chemical | ChemComp-DMY / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.15 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE |
Detector | Type: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Nov 3, 1994 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.6 Å / Num. all: 1770 / Num. obs: 1291 / % possible obs: 73 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Rsym value: 0.014 |
Reflection | *PLUS % possible obs: 73 % / Rmerge(I) obs: 0.014 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: GDHB25 Highest resolution: 1.9 Å / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 10.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|