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- PDB-1hhx: Solution structure of LNA3:RNA hybrid -

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Basic information

Entry
Database: PDB / ID: 1hhx
TitleSolution structure of LNA3: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
KeywordsANTISENSE / LOCKED NUCLEIC ACID / LNA / RNA / HYBRID / RNASE H
Function / homologyDNA/RNA hybrid / RNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsPetersen, M. / Bondensgaard, K. / Wengel, J. / Jacobsen, J.P.
Citation
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.
#1: 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.
History
DepositionDec 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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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)5,6712
Polymers5,6712
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)34 / 40LOWEST ENERGY
RepresentativeModel #11

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Components

#1: DNA/RNA hybrid 5- D(*CP*+TP*GP*AP*+TP*AP*+TP*GP*C) -3


Mass: 2814.843 Da / Num. of mol.: 1 / Source method: obtained synthetically
#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
Sequence detailsCHAIN A RESIDUES 2,5,7 ARE LOCKED NUCLEIC ACIDS OR (1R,3R,4R,7S)-7-HYDROXY-1-HYDROXYMETHYL-3- ...CHAIN A RESIDUES 2,5,7 ARE LOCKED NUCLEIC ACIDS OR (1R,3R,4R,7S)-7-HYDROXY-1-HYDROXYMETHYL-3-(THYMIN-1-YL)- 2,5-DIOXABICYCLO[2.2.1]HEPTANE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

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Sample preparation

DetailsContents: 0.7E-3M LNA1:RNA, 0.1M NACL, 5E-5M EDTA AND 1E-2M PHOSPHATE BUFFER IN 100% D2O
Sample conditionsIonic strength: 0.1 / pH: 7 / 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 423 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE PROGRAM RANDMARDI. A FURTHER 58 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM NOESY IN H2O ...Details: A TOTAL OF 423 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE PROGRAM RANDMARDI. A FURTHER 58 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM NOESY IN H2O USING ISPA. 22 WATSON-CRICK BASE PAIRING RESTRAINTS.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 34

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