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- PDB-4dkz: Hairpin structure of a DNA dodecamer containing North-methanocarb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dkz | ||||||
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Title | Hairpin structure of a DNA dodecamer containing North-methanocarba-2'-deoxythymidine | ||||||
![]() | Synthetic DNA dodecamer containg North-methanocarba-2'-deoxythymidine (N-MCdT) | ||||||
![]() | DNA / North-methanocarba-2'-deoxythymidine / N-MCdT / X-ray crystal structure / tetra-loop hairpin / C4'-exo pucker / hairpin DNA | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Egli, M. / Pallan, P.S. | ||||||
![]() | ![]() Title: The Conformationally Constrained N-Methanocarba-dT Analogue Adopts an Unexpected C4'-exo Sugar Pucker in the Structure of a DNA Hairpin. Authors: Pallan, P.S. / Marquez, V.E. / Egli, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.2 KB | Display | ![]() |
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PDB format | ![]() | 15 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.9 KB | Display | ![]() |
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Full document | ![]() | 389.3 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5.7 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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Unit cell |
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Components
#1: DNA chain | Mass: 3683.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized nucleic acid dodecamer #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 40 mM sodium cacodylate, pH 6.0, 80 mM sodium chloride, 12 mM spermine tetrahydrochloride and 10% v/v 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2008 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 5865 / Num. obs: 5795 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.032 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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