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- PDB-1d56: ALTERNATIVE STRUCTURES FOR ALTERNATING POLY(DA-DT) TRACTS: THE ST... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d56 | ||||||||||||||||||
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Title | ALTERNATIVE STRUCTURES FOR ALTERNATING POLY(DA-DT) TRACTS: THE STRUCTURE OF THE B-DNA DECAMER C-G-A-T-A-T-A-T-C-G | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / DOUBLE HELIX | Function / homology | DNA | ![]() Method | ![]() ![]() Yuan, H. / Quintana, J. / Dickerson, R.E. | ![]() ![]() Title: Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G. Authors: Yuan, H. / Quintana, J. / Dickerson, R.E. #1: ![]() 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. #2: ![]() Title: Analysis of Local Helix Geometry in Three B-DNA Decamers and Eight Dodecamers Authors: Yanagi, K. / Prive, G.G. / Dickerson, R.E. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.6 KB | Display | ![]() |
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PDB format | ![]() | 14.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 371.2 KB | Display | ![]() |
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Full document | ![]() | 381.1 KB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-CA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.81 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: pH 6.90, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.9 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→8 Å / Num. all: 6166 / Num. obs: 3683 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Observed criterion σ(F): 2 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 25 % |
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Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||
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Refinement | Resolution: 1.7→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.178 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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