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- PDB-2n4j: Solution structure of a self complementary Xylonucleic Acid duplex -

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Basic information

Entry
Database: PDB / ID: 2n4j
TitleSolution structure of a self complementary Xylonucleic Acid duplex
ComponentsXNA (5'-R(*(8XG)P*(8XU)P*(8XG)P*(8XU)P*(8XA)P*(8XC)P*(8XA)P*(8XC))-3')
KeywordsUNKNOWN FUNCTION
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsclosest to the average, model1
AuthorsMaiti, M. / Lescrinier, E. / Herdewijn, P.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Xylonucleic acid: synthesis, structure, and orthogonal pairing properties.
Authors: Maiti, M. / Maiti, M. / Knies, C. / Dumbre, S. / Lescrinier, E. / Rosemeyer, H. / Ceulemans, A. / Herdewijn, P.
History
DepositionJun 19, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XNA (5'-R(*(8XG)P*(8XU)P*(8XG)P*(8XU)P*(8XA)P*(8XC)P*(8XA)P*(8XC))-3')
B: XNA (5'-R(*(8XG)P*(8XU)P*(8XG)P*(8XU)P*(8XA)P*(8XC)P*(8XA)P*(8XC))-3')


Theoretical massNumber of molelcules
Total (without water)5,0532
Polymers5,0532
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain XNA (5'-R(*(8XG)P*(8XU)P*(8XG)P*(8XU)P*(8XA)P*(8XC)P*(8XA)P*(8XC))-3')


Mass: 2526.561 Da / Num. of mol.: 2 / 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 TOCSY
1312D 1H-1H NOESY
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic
1612D 1H-13C HMBC aromatic
1722D 1H-1H NOESY
1812D 1H-31P COSY
19131P Dec. 2D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM XNA, 100% D2O100% D2O
21.5 mM XNA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMXNA-11
1.5 mMXNA-22
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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