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Open data
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Basic information
Entry | Database: PDB / ID: 1zyf | ||||||||||||||||||||
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Title | Structure of a Supercoiling Responsive DNA Site | ||||||||||||||||||||
![]() | 5'-D(*![]() DNA / Supercoiling / Hix / recombinase / Hin | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / simulated annealing, torsion angle dynamics (XPLOR-NIH) | Model type details | minimized average | ![]() Bae, S.H. / Yun, S.H. / Sun, D. / Lim, H.M. / Choi, B.S. | ![]() ![]() Title: Structural and dynamic basis of a supercoiling-responsive DNA element Authors: Bae, S.H. / Yun, S.H. / Sun, D. / Lim, H.M. / Choi, B.S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 383.3 KB | Display | ![]() |
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PDB format | ![]() | 320 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 308.6 KB | Display | ![]() |
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Full document | ![]() | 441 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 17.8 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: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid-support Phosphoramidite Chemistry |
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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 conditions | Ionic strength: 10mM sodium phosphate, 100mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 295 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics (XPLOR-NIH) Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||
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: 100 / Conformers submitted total number: 26 |