+Open data
-Basic information
Entry | Database: PDB / ID: 1hoq | ||||||||||||||||||
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Title | CHIMERIC RNA/DNA HAIRPIN | ||||||||||||||||||
Components | DNA/RNA (5'-R(*Keywords | DNA / RNA / Hairpin | Function / homology | DNA/RNA hybrid / DNA/RNA hybrid (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Authors | Denisov, A.Y. / Gehring, K. | Citation | Journal: Nucleic Acids Res. / Year: 2001 Title: Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids. Authors: Denisov, A.Y. / Noronha, A.M. / Wilds, C.J. / Trempe, J.F. / Pon, R.T. / Gehring, K. / Damha, M.J. #1: Journal: NUCLEOSIDES NUCLEOTIDES NUCLEIC ACIDS / Year: 2001 Title: Properties of Arabinonucleic Acids (ANA & 2'F-ANA): Implications for the Design of Antisense Therapeutics that Invoke RNase H Cleavage of RNA Authors: Damha, M.J. / Noronha, A.M. / Wilds, C.J. / Trempe, J.F. / Denisov, A.Y. / Pon, R.T. / Gehring, K. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hoq.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hoq.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hoq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hoq_validation.pdf.gz | 305 KB | Display | wwPDB validaton report |
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Full document | 1hoq_full_validation.pdf.gz | 351.1 KB | Display | |
Data in XML | 1hoq_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1hoq_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/1hoq ftp://data.pdbj.org/pub/pdb/validation_reports/ho/1hoq | 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/RNA hybrid | Mass: 3718.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase synthesis, phosphoramidite chemistry |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homo- and heteronuclear techniques: 2D-NOESY, DQF-COSY, TOCSY, H,C-HMQC, H,P-HetCOSY |
-Sample preparation
Details |
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Sample conditions | pH: 7 / Pressure: 1 atm / Temperature: 293 K | |||||||||
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: 500 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures were refined by NMR-restrained molecular dynamics (14 ps, 300-1000 K) with final energy minimization | ||||||||||||
NMR representative | Selection criteria: the hairpin stem structure closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |