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- PDB-2oj8: NMR structure of the UGUU tetraloop of Duck Epsilon apical stem l... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oj8 | ||||||||||||||||||
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Title | NMR structure of the UGUU tetraloop of Duck Epsilon apical stem loop of the Hepatitis B virus | ||||||||||||||||||
![]() | 5'-R(P*![]() RNA / HBV / epsilon / Duck / UGUU / tetraloop | Function / homology | RNA | ![]() Method | SOLUTION NMR / Torsion angle dynamics with chemical shift refinement using XPLOR 8.351 with home written refinement chemical shift refinement module | ![]() Girard, F.C. / Ottink, O.M. / Ampt, K.A.M. / Tessari, M. / Wijmenga, S.S. | ![]() ![]() Title: Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals. Authors: Girard, F.C. / Ottink, O.M. / Ampt, K.A. / Tessari, M. / Wijmenga, S.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 | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 34.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 319.9 KB | Display | ![]() |
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Full document | ![]() | 357.1 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.5 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: RNA chain | Mass: 2520.505 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The Sequence of this RNA can be found in Duck Hepatitis B virus |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: In addition TOCSY spectra and 31P 1D and 31P HMBC spectra were recorded |
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Sample preparation
Details |
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Sample conditions |
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-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 | Name: ![]() Developer: Girard, F.C., Ottink O.M., Ampt, K.A.M., Tessari, M., Wijmenga, S.S. Classification: refinement |
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Refinement | Method: Torsion angle dynamics with chemical shift refinement using XPLOR 8.351 with home written refinement chemical shift refinement module Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |