[English] 日本語
Yorodumi- PDB-187d: HYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 187d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | HYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYSTAL STRUCTURES. IMPLICATIONS FOR DNA RECOGNITION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | Authors | Eisenstein, M. / Shakked, Z. | Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. Authors: Eisenstein, M. / Shakked, Z. #1: Journal: J.Biomol.Struct.Dyn. / Year: 1987 Title: The Crystal Structure of d(CCCCGGGG): A New A-Form Variant with an Extended Backbone Conformation Authors: Haran, T.E. / Shakked, Z. / Wang, A.H.-J. / Rich, A. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 187d.cif.gz | 12.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb187d.ent.gz | 7.7 KB | Display | PDB format |
PDBx/mmJSON format | 187d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/87/187d ftp://data.pdbj.org/pub/pdb/validation_reports/87/187d | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: DNA chain | Mass: 2428.593 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: unknownDetails: Wang, A. H.-J., (1982) Proc. Nat. Acad. Sci. USA., 79, 3968. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 288 K |
---|---|
Detector | Type: NICOLET / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å |
Reflection | *PLUS Highest resolution: 2.25 Å |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.25→8 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.134 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |