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Open data
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Basic information
Entry | Database: PDB / ID: 1ezn | ||||||
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Title | SOLUTION STRUCTURE OF A DNA THREE-WAY JUNCTION | ||||||
![]() | DNA THREE-WAY JUNCTION | ||||||
![]() | DNA / three-way junction / four-way junction / HMG-box protein / Holliday junction / hammerhead | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
![]() | van Buuren, B.N.M. / Overmars, F.J. / Ippel, J.H. / Altona, C. / Wijmenga, S.S. | ||||||
![]() | ![]() Title: Solution structure of a DNA three-way junction containing two unpaired thymidine bases. Identification of sequence features that decide conformer selection. Authors: van Buuren, B.N. / Overmars, F.J. / Ippel, J.H. / Altona, C. / Wijmenga, S.S. #1: ![]() Title: NMR studies of DNA three-way junctions containing two unpaired thymidine bases: the influence of the sequence at the junction on the stability of the stacking conformers. Authors: Overmars, F.J. / Pikkemaat, J.A. / van den Elst, H. / van Boom, J.H. / Altona, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 591.2 KB | Display | ![]() |
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PDB format | ![]() | 490.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 306.7 KB | Display | ![]() |
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Full document | ![]() | 452.2 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 32.6 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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NMR ensembles |
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Components
#1: DNA chain | Mass: 11053.049 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
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Sample preparation
Details | Contents: 1mM DNA 3H; 50mM NaCl; / Solvent system: D2O/H2O and D2O |
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Sample conditions | Ionic strength: 50mM / pH: 7 / Pressure: 1 atm / Temperature: 293 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz |
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Processing
NMR software | Name: ![]() |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 26 |