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- PDB-2d25: C-C-A-G-G-C-M5C-T-G-G; HELICAL FINE STRUCTURE, HYDRATION, AND COM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2d25 | ||||||||||||||||||
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Title | C-C-A-G-G-C-M5C-T-G-G; HELICAL FINE STRUCTURE, HYDRATION, AND COMPARISON WITH C-C-A-G-G-C-C-T-G-G | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | ![]() Method | ![]() ![]() Heinemann, U. / Hahn, M. | ![]() ![]() Title: C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G. Authors: Heinemann, U. / Hahn, M. #1: ![]() Title: The Conformation of a B-DNA Decamer Is Mainly Determined By Its Sequence and Not By Crystal Environment Authors: Heinemann, U. / Alings, C. #2: ![]() Title: Crystallographic Study of One Turn of G/C-Rich B-DNA Authors: Heinemann, U. / Alings, C. #3: ![]() Title: Structural Features of G/C-Rich DNA Going a Or B Authors: Heinemann, U. / Alings, C. / Lauble, H. #4: ![]() Title: X-Ray Studies of DNA Aiming at Elucidating the Sequence-Structure Code Authors: Heinemann, U. / Alings, C. / Lauble, H. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.6 KB | Display | ![]() |
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PDB format | ![]() | 15.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.4 KB | Display | ![]() |
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Full document | ![]() | 387.3 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: 3060.020 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 7.5 / Details: pH 7.50, MICRODIALYSIS, temperature 277.00K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 Details: referred to 'Heinemann, U.', (1991) 'Embo J.', 10, 35-43 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→8 Å / Num. all: 7209 / Num. obs: 4704 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 8 Å / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0385 |
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Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.75→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.75→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 8 Å / Num. reflection obs: 3799 / σ(F): 2 / Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |