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- PDB-1hg9: Solution structure of DNA:RNA hybrid -

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Basic information

Entry
Database: PDB / ID: 1hg9
TitleSolution structure of DNA:RNA hybrid
Components
  • 5- D(*CP*TP*GP*AP*TP*AP*TP*GP*C) -3
  • 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3
KeywordsDNA-RNA HYBRID / DNA RNA HYBRID / DNA/RNA CHIMERIC HYBRID DUPLEX / ANTISENSE / LOCKED NUCLEIC ACID / DNA / RNA / HYBRID / RNASE H
Function / homologyDNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsPetersen, 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
DepositionDec 13, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy
Category: citation / pdbx_database_status ...citation / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5- D(*CP*TP*GP*AP*TP*AP*TP*GP*C) -3
B: 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3


Theoretical massNumber of molelcules
Total (without water)5,5872
Polymers5,5872
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 40
RepresentativeModel #20

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Components

#1: DNA chain 5- D(*CP*TP*GP*AP*TP*AP*TP*GP*C) -3


Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3


Mass: 2855.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

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Sample preparation

DetailsContents: 2.0E-3M DNA:RNA, 0.1M NACL, 5E-5M EDTA AND 1E-2M PHOSPHATE BUFFER IN 100% D2O
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCASE, DA, KOLLMAN, PArefinement
MARDIGRASstructure solution
Amberstructure solution
Felixstructure solution
RefinementMethod: 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 ensembleConformers calculated total number: 40 / Conformers submitted total number: 40

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