+Open data
-Basic information
Entry | Database: PDB / ID: 2kp4 | ||||||
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Title | Structure of 2'F-ANA/RNA hybrid duplex | ||||||
Components |
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Keywords | DNA/RNA / 2-deoxy-2-fluoro-D-arabinose / FANA / nucleic acid structure / NMR/MD/TI / hybrid duplex / DNA-RNA complex | ||||||
Function / homology | DNA / RNA Function and homology information | ||||||
Method | SOLUTION NMR / molecular dynamics, matrix relaxation | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Gonzalez, C. / Martin-Pintado, N. / Watts, J. / Gomez-Pinto, I. / Dhama, M. / Orozco, M. / Schwartzentruber, J. / Portella, G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2010 Title: Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Authors: Watts, J.K. / Martin-Pintado, N. / Gomez-Pinto, I. / Schwartzentruber, J. / Portella, G. / Orozco, M. / Gonzalez, C. / Damha, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kp4.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kp4.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 2kp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kp4_validation.pdf.gz | 334.7 KB | Display | wwPDB validaton report |
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Full document | 2kp4_full_validation.pdf.gz | 411.1 KB | Display | |
Data in XML | 2kp4_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2kp4_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/2kp4 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/2kp4 | HTTPS FTP |
-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: 3263.947 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 3121.908 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8 mM FANA/RNA-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.8 mM / Component: FANA/RNA-1 |
Sample conditions | pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Advance / Manufacturer: Bruker / Model: Advance / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics, matrix relaxation / Software ordinal: 1 | ||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |