+Open data
-Basic information
Entry | Database: PDB / ID: 1hg9 | ||||||
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Title | Solution structure of DNA:RNA hybrid | ||||||
Components |
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Keywords | DNA-RNA HYBRID / DNA RNA HYBRID / DNA/RNA CHIMERIC HYBRID DUPLEX / ANTISENSE / LOCKED NUCLEIC ACID / DNA / RNA / HYBRID / RNASE H | ||||||
Function / homology | DNA / RNA Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Petersen, M. / Bondensgaard, K. / Wengel, J. / Jacobsen, J.P. | ||||||
Citation | Journal: Chemistry / Year: 2000 Title: Structural studies of LNA:RNA duplexes by NMR: conformations and implications for RNase H activity. Authors: Bondensgaard, K. / Petersen, M. / Singh, S.K. / Rajwanshi, V.K. / Kumar, R. / Wengel, J. / Jacobsen, J.P. #1: Journal: J.Mol.Recognit. / Year: 2000 Title: The Conformations of Locked Nucleic Acids (Lna) Authors: Petersen, M. / Nielsen, C.B. / Nielsen, K.E. / Jensen, G.A. / Bondensgaard, K. / Singh, S.K. / Rajwanshi, V.K. / Koshkin, A.A. / Dahl, B.M. / Wengel, J. / Jacobsen, J.P. #2: Journal: J.Am.Chem.Soc. / Year: 2002 Title: Locked Nucleic Acid (Lna) Recognition of RNA: NMR Solution Structures of Lna:RNA Hybrids Authors: Petersen, M. / Bondensgaard, K. / Wengel, J. / Jacobsen, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hg9.cif.gz | 450.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hg9.ent.gz | 370.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/1hg9 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/1hg9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 2855.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: NOESY |
-Sample preparation
Details | Contents: 2.0E-3M DNA:RNA, 0.1M NACL, 5E-5M EDTA AND 1E-2M PHOSPHATE BUFFER IN 100% D2O |
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Sample conditions | Ionic strength: 0.1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: A TOTAL OF 354 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE PROGRAM RANDMARDI. 22 WATSON-CRICK BASE PAIRING RESTRAINTS. | |||||||||||||||
NMR ensemble | Conformers calculated total number: 40 / Conformers submitted total number: 40 |