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Basic information
Entry | Database: PDB / ID: 2m54 | ||||||||||||||||||
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Title | Refined NMR solution structure of metal-modified DNA | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / artificial nucleobase / imidazole nucleoside | Function / homology | SILVER ION / DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / torsion angle dynamics | ![]() Kumbhar, S. / Johannsen, S. / Sigel, R.K. / Waller, M.P. / Mueller, J. | ![]() ![]() Title: A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs. Authors: Kumbhar, S. / Johannsen, S. / Sigel, R.K. / Waller, M.P. / Muller, J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 405.9 KB | Display | ![]() |
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PDB format | ![]() | 343.2 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 540.2 KB | Display | ![]() |
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Full document | ![]() | 801.4 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Assembly
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NMR ensembles |
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Components
#1: DNA chain | Mass: 5015.311 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample |
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-NMR measurement
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Processing
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 34 / NA beta-angle constraints total count: 34 / NA chi-angle constraints total count: 28 / NA delta-angle constraints total count: 28 / NA epsilon-angle constraints total count: 34 / NA gamma-angle constraints total count: 34 / NA other-angle constraints total count: 0 / NOE constraints total: 848 / NOE intraresidue total count: 366 / NOE long range total count: 15 / NOE medium range total count: 25 / NOE sequential total count: 442 / Hydrogen bond constraints total count: 56 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.2 Å |