+Open data
-Basic information
Entry | Database: PDB / ID: 1zyf | ||||||||||||||||||||
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Title | Structure of a Supercoiling Responsive DNA Site | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Supercoiling / Hix / recombinase / Hin | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, torsion angle dynamics (XPLOR-NIH) | Model type details | minimized average | Authors | Bae, S.H. / Yun, S.H. / Sun, D. / Lim, H.M. / Choi, B.S. | Citation | Journal: Nucleic Acids Res. / Year: 2006 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zyf.cif.gz | 382.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zyf.ent.gz | 332.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/1zyf ftp://data.pdbj.org/pub/pdb/validation_reports/zy/1zyf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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
Details |
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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 |