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Yorodumi- PDB-206d: BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 206d | ||||||
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Title | BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED IN THE CRYSTAL STRUCTURE OF A GAL OPERON FRAGMENT: IMPLICATIONS FOR PROTEIN-DNA RECOGNITION | ||||||
Components |
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Keywords | DNA / B-DNA / DOUBLE HELIX | ||||||
Function / homology | SPERMINE / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Tari, L.W. / Secco, A.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 1995 Title: Base-pair opening and spermine binding--B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition. Authors: Tari, L.W. / Secco, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 206d.cif.gz | 18.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb206d.ent.gz | 10.9 KB | Display | PDB format |
PDBx/mmJSON format | 206d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 206d_validation.pdf.gz | 336 KB | Display | wwPDB validaton report |
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Full document | 206d_full_validation.pdf.gz | 350.1 KB | Display | |
Data in XML | 206d_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 206d_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/06/206d ftp://data.pdbj.org/pub/pdb/validation_reports/06/206d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 1865.240 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 1754.182 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.58 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Detector | Type: RIGAKU AFC-6S / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 1233 / Observed criterion σ(F): 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→20 Å / σ(F): 1 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |