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Yorodumi- PDB-1da3: THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1da3 | ||||||||||||||||||
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Title | THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Baikalov, I. / Grzeskowiak, K. / Yanagi, K. / Quintana, J. / Dickerson, R.E. | Citation | Journal: J.Mol.Biol. / Year: 1993 Title: The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn. Authors: Baikalov, I. / Grzeskowiak, K. / Yanagi, K. / Quintana, J. / Dickerson, R.E. #1: Journal: J.Biol.Chem. / Year: 1991 Title: The Structure of B-Helical C-G-A-T-C-G-A-T-C-G and Comparison with C-C-A-A-C-G- T-T-G-G. The Effect of Base Pair Reversals Authors: Grzeskowiak, K. / Yanagi, K. / Prive, G.G. / Dickerson, R.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1da3.cif.gz | 24.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1da3.ent.gz | 14.4 KB | Display | PDB format |
PDBx/mmJSON format | 1da3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1da3_validation.pdf.gz | 376 KB | Display | wwPDB validaton report |
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Full document | 1da3_full_validation.pdf.gz | 396.5 KB | Display | |
Data in XML | 1da3_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1da3_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1da3 ftp://data.pdbj.org/pub/pdb/validation_reports/da/1da3 | 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: 3059.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #2: Chemical | ChemComp-CL / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.39 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→8 Å / Num. obs: 2282 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Observed criterion σ(I): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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