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- PDB-1h0q: NMR solution structure of a fully modified locked nucleic acid (L... -

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Basic information

Entry
Database: PDB / ID: 1h0q
TitleNMR solution structure of a fully modified locked nucleic acid (LNA) hybridized to RNA
Components
  • 5-D(*(LKC)P*(TLN)P*(LCG)P*(LCA)P*(TLN)P*(LCA)P* (TLN)P*(LCG)P*(LCC))-3
  • 5-R(*GP*CP*AP*UP*AP*UP*CP*AP*G)-3
KeywordsDNA-RNA HYBRID / LNA / RNA / LOCKED NUCLEIC ACID / HYBRID / DNA/RNA HYBRID
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsRasmussen, J. / Petersen, M. / Nielsen, K.E. / Kumar, R. / Wengel, J. / Jacobsen, J.P.
CitationJournal: Bioconjug.Chem. / Year: 2004
Title: NMR Studies of Fully Modified Locked Nucleic Acid (Lna) Hybrids: Solution Structure of an Lna:RNA Hybrid and Characterization of an Lna:RNA Hybrid
Authors: Nielsen, K.E. / Rasmussen, J. / Kumar, R. / Wengel, J. / Jacobsen, J.P. / Petersen, M.
History
DepositionJun 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2003Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_mr / _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(*(LKC)P*(TLN)P*(LCG)P*(LCA)P*(TLN)P*(LCA)P* (TLN)P*(LCG)P*(LCC))-3
B: 5-R(*GP*CP*AP*UP*AP*UP*CP*AP*G)-3


Theoretical massNumber of molelcules
Total (without water)5,7872
Polymers5,7872
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)20 / 20
RepresentativeModel #17

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Components

#1: RNA chain 5-D(*(LKC)P*(TLN)P*(LCG)P*(LCA)P*(TLN)P*(LCA)P* (TLN)P*(LCG)P*(LCC))-3


Mass: 2930.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FULLY MODIFIED LNA STRAND
#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 detailsLKC IS SIMILAR TO LCC EXCEPT THAT IT DOES NOT HAVE A 5' PHOSPHATE GROUP.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
141HSQC
NMR detailsText: SEE REFERENCE FOR FURTHER DETAILS

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Sample preparation

DetailsContents: 2 MM NUCLEIC ACID, 100MM NACL, 10 MM PHOSPHATE BUFFER
Sample conditionspH: 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: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCASE ET AL.refinement
Felixstructure solution
Amberstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformers calculated total number: 20 / Conformers submitted total number: 20

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