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- PDB-2mfd: The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Ent... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2mfd | ||||||||||||||||||||||
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Title | The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03 | ||||||||||||||||||||||
![]() | 5'-R(P*![]() RNA / 5'-NTR / cloverleaf | Function / homology | RNA / RNA (> 10) | ![]() Biological species | ![]() Method | SOLUTION NMR / simulated annealing, distance geometry | Model details | closest to the average, model1 | ![]() Ihle, Y. / Zell, R. / Gorlach, M. | ![]() ![]() Title: The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir 404/03 Authors: Ihle, Y. / Zell, R. / Gorlach, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.4 KB | Display | ![]() |
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PDB format | ![]() | 197.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 535.7 KB | Display | ![]() |
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Full document | ![]() | 686 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: RNA chain | Mass: 6070.633 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA polymerase Source: (synth.) ![]() |
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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 |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing, distance geometry / Software ordinal: 1 / Details: refinement in water based on ARIA scripts | ||||||||||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 18 / NA beta-angle constraints total count: 18 / NA chi-angle constraints total count: 19 / NA delta-angle constraints total count: 19 / NA epsilon-angle constraints total count: 18 / NA gamma-angle constraints total count: 19 / NA other-angle constraints total count: 18 / NA sugar pucker constraints total count: 19 / NOE constraints total: 587 / NOE intraresidue total count: 268 / NOE long range total count: 59 / NOE medium range total count: 17 / NOE sequential total count: 243 / Hydrogen bond constraints total count: 36 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |