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- PDB-2kp3: Structure of ANA-RNA hybrid duplex -

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Basic information

Entry
Database: PDB / ID: 2kp3
TitleStructure of ANA-RNA hybrid duplex
Components
  • RNA (5'-R(*(GAO)P*(CAR)P*(UAR)P*(A5O)P*(UAR)P*(A5O)P*(A5O)P*(UAR)P*(GAO)P*(GAO))-3')
  • RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3')
KeywordsRNA / ANA / arabinonucleic acid / nucleic acid structure / NMR/MD/TI / hybrid duplex
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics, matrix relaxation
Model detailslowest energy, model 1
AuthorsGonzalez, C. / Martn-Pintado, N. / Watts, J. / Gomez-Pinto, I. / Dhama, M. / Orozco, M. / Schwartzentruber, J. / Portella, G.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.
Authors: Watts, J.K. / Martin-Pintado, N. / Gomez-Pinto, I. / Schwartzentruber, J. / Portella, G. / Orozco, M. / Gonzalez, C. / Damha, M.J.
History
DepositionOct 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*(GAO)P*(CAR)P*(UAR)P*(A5O)P*(UAR)P*(A5O)P*(A5O)P*(UAR)P*(GAO)P*(GAO))-3')
B: RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,3242
Polymers6,3242
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)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*(GAO)P*(CAR)P*(UAR)P*(A5O)P*(UAR)P*(A5O)P*(A5O)P*(UAR)P*(GAO)P*(GAO))-3')


Mass: 3201.957 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3')


Mass: 3121.908 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 0.8 mM ANA/RNA hybrid duplex-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: ANA/RNA hybrid duplex-1
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Advance / Manufacturer: Bruker / Model: Advance / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmdata analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
AmberGoddardrefinement
AmberGoddarddata analysis
AmberGoddardstructure solution
AmberKoradi, Billeter and Wuthrichrefinement
AmberKoradi, Billeter and Wuthrichdata analysis
AmberKoradi, Billeter and Wuthrichstructure solution
RefinementMethod: molecular dynamics, matrix relaxation / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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