[English] 日本語
Yorodumi- PDB-252d: CRYSTAL STRUCTURE OF THE B-DNA DECAMER D(CGCAATTGCG)2; SEQUENCE-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 252d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE B-DNA DECAMER D(CGCAATTGCG)2; SEQUENCE-DEPENDENT CROSSED HELIX PACKING | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | Authors | Wood, A.A. / Nunn, C.M. / Trent, J.O. / Neidle, S. | Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Sequence-dependent crossed helix packing in the crystal structure of a B-DNA decamer yields a detailed model for the Holliday junction. Authors: Wood, A.A. / Nunn, C.M. / Trent, J.O. / Neidle, S. #1: Journal: Biochemistry / Year: 1995 Title: Crystal Structure of C-T-C-T-C-G-A-G-A-G. Implications for the Structure of the Holliday Junction Authors: Goodsell, D.S. / Grzeskowiak, K. / Dickerson, R.E. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 252d.cif.gz | 21.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb252d.ent.gz | 13.7 KB | Display | PDB format |
PDBx/mmJSON format | 252d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 252d_validation.pdf.gz | 323.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 252d_full_validation.pdf.gz | 329.9 KB | Display | |
Data in XML | 252d_validation.xml.gz | 2.2 KB | Display | |
Data in CIF | 252d_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/52/252d ftp://data.pdbj.org/pub/pdb/validation_reports/52/252d | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 292.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
---|---|
Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: Aug 3, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→8 Å / Num. all: 5015 / Num. obs: 2304 / % possible obs: 78 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.043 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 4 Å / % possible obs: 78 % / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.34 Å / % possible obs: 40.2 % / Rmerge(I) obs: 0.131 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.3→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|