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Open data
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Basic information
Entry | Database: PDB / ID: 1idx | ||||||||||||||||||
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Title | Structural Basis for Poor Excision from Hairpin DNA: NMR Study | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Uracil / Hairpin DNA / Hairpin loop / Double helix / UDG-Uracil interaction | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / Restrained molecular dynamics, Energy minimization | ![]() Ghosh, M. / Rumpal, N. / Varshney, U. / Chary, K.V. | ![]() ![]() Title: Structural basis for poor uracil excision from hairpin DNA. An NMR study. Authors: Ghosh, M. / Rumpal, N. / Varshney, U. / Chary, K.V. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.6 KB | Display | ![]() |
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PDB format | ![]() | 58.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 306.6 KB | Display | ![]() |
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Full document | ![]() | 329 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ii1C C: citing same article ( |
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Links
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Assembly
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NMR ensembles |
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Components
#1: DNA chain | Mass: 5483.537 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Custom made by Ransom Hill Biosciences, Inc., Ramona CA (USA) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using 2D homonuclear techniques |
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Sample preparation
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
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Refinement | Method: Restrained molecular dynamics, Energy minimization / Software ordinal: 1 Details: The structures are based on a total of 196 restraints, 122 are NOE-derived distance constraints, 64 dihedral angle restraints, 10 distance restraints from hydrogen bonds. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations,lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 6 |