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Open data
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Basic information
Entry | Database: PDB / ID: 1q8n | ||||||
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Title | Solution Structure of the Malachite Green RNA Binding Aptamer | ||||||
![]() | RNA Aptamer | ||||||
![]() | RNA / rna aptamer / malachite green / base triple / base quadruple / rna ligand interactions | ||||||
Function / homology | MALACHITE GREEN / RNA / RNA (> 10)![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Flinders, J. / DeFina, S.C. / Brackett, D.M. / Baugh, C. / Wilson, C. / Dieckmann, T. | ||||||
![]() | ![]() Title: Recognition of planar and nonplanar ligands in the malachite green-RNA aptamer complex. Authors: Flinders, J. / DeFina, S.C. / Brackett, D.M. / Baugh, C. / Wilson, C. / Dieckmann, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 606.3 KB | Display | ![]() |
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PDB format | ![]() | 509.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 407 KB | Display | ![]() |
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Full document | ![]() | 574 KB | Display | |
Data in XML | ![]() | 54 KB | Display | |
Data in CIF | ![]() | 84.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: RNA chain | Mass: 12317.421 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence was synthesized in vitro and does not occur naturally. |
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#2: Chemical | ChemComp-MGR / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined with the aid of the crystal structure of a similar RNA aptamer. |
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Sample preparation
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structure was based on 423 NOE constraints (148 intranucleotide, 119 sequential, 66 medium to long range, and 90 RNA to ligand NOEs) and 219 dihedral angle restraints. | ||||||||||||||||||||
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: 25 |