+Open data
-Basic information
Entry | Database: PDB / ID: 2kd4 | ||||||||||||||||||||
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Title | Solution structure and thermodynamics of 2',5' RNA intercalation | ||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / proflavine / intercalation / 2' / 5' RNA / nearest-neighbor exclusion | Function / homology | PROFLAVIN / RNA | Function and homology information Method | SOLUTION NMR / simulated annealing | Model details | lowest energy, model 1 | Authors | Horowitz, E.D. / Lilavivat, S. / Holladay, B.W. / Germann, M.W. / Hud, N.V. | Citation | Journal: J.Am.Chem.Soc. / Year: 2009 | Title: Solution structure and thermodynamics of 2',5' RNA intercalation. Authors: Horowitz, E.D. / Lilavivat, S. / Holladay, B.W. / Germann, M.W. / Hud, N.V. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kd4.cif.gz | 19.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kd4.ent.gz | 13.2 KB | Display | PDB format |
PDBx/mmJSON format | 2kd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kd4_validation.pdf.gz | 329.8 KB | Display | wwPDB validaton report |
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Full document | 2kd4_full_validation.pdf.gz | 329.7 KB | Display | |
Data in XML | 2kd4_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 2kd4_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/2kd4 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/2kd4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 2556.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 2',5' RNA #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4, 99.9% D2O Solvent system: 99.9% D2O | |||||||||||||||
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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 / Software ordinal: 1 Details: 300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealed | ||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 14 / NA other-angle constraints total count: 14 / NOE constraints total: 378 / NOE intraresidue total count: 258 / NOE medium range total count: 378 / NOE sequential total count: 258 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10 / Conformers submitted total number: 1 |