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Open data
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Basic information
Entry | Database: PDB / ID: 1jrv | ||||||
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Title | SOLUTION STRUCTURE OF DAATAA DNA BULGE | ||||||
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![]() | DNA / DNA BULGE / FIVE-NUCLEOTIDE BULGE LOOP / DEOXYRIBONUCLEIC ACID | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / matrix relaxation (MARDIGRAS); torsion angle dynamics (DYANA); ENERGY MINIMIZATION (AMBER) | ||||||
![]() | Gollmick, F.A. / Lorenz, M. / Dornberger, U. / von Langen, J. / Diekmann, S. / Fritzsche, H. | ||||||
![]() | ![]() Title: Solution structure of dAATAA and dAAUAA DNA bulges. Authors: Gollmick, F.A. / Lorenz, M. / Dornberger, U. / von Langen, J. / Diekmann, S. / Fritzsche, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.3 KB | Display | ![]() |
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PDB format | ![]() | 222.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 321.1 KB | Display | ![]() |
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Full document | ![]() | 461.9 KB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 11.6 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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NMR ensembles |
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Components
#1: DNA chain | Mass: 5220.412 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-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 standard 2D homonuclear and heteronuclear 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
NMR software |
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Refinement | Method: matrix relaxation (MARDIGRAS); torsion angle dynamics (DYANA); ENERGY MINIMIZATION (AMBER) Software ordinal: 1 Details: the structures are based on a total of 906 restraints, 645 are NOE-derived distance constraints, 235 dihedral angle restraints, 26 distance restraints from hydrogen bonds. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 15 |