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- PDB-2lsc: Solution structure of 2'F-ANA and ANA self-complementary duplex -

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Basic information

Entry
Database: PDB / ID: 2lsc
TitleSolution structure of 2'F-ANA and ANA self-complementary duplex
ComponentsDNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL)P*(A5O)P*(A5O)P*(UAR)P*(UAR)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')
KeywordsDNA / Dickerson Drew dodecamer
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 13
AuthorsMartin-Pintado, N. / Yahyaee, M. / Campos, R. / Noronha, A. / Wilds, C. / Damha, M. / Gonzalez, C.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion.
Authors: Martin-Pintado, N. / Yahyaee-Anzahaee, M. / Campos-Olivas, R. / Noronha, A.M. / Wilds, C.J. / Damha, M.J. / Gonzalez, C.
History
DepositionApr 26, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: 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: DNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL)P*(A5O)P*(A5O)P*(UAR)P*(UAR)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')
B: DNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL)P*(A5O)P*(A5O)P*(UAR)P*(UAR)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')


Theoretical massNumber of molelcules
Total (without water)7,6872
Polymers7,6872
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 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL)P*(A5O)P*(A5O)P*(UAR)P*(UAR)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')


Mass: 3843.264 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 1H-1H NOESY
1222D 1H-1H TOCSY
1322D DQF-COSY
1422D 1H-19F HOESY
1522D 1H-1H NOESY
1612D 1H-1H TOCSY
2712D 1H-1H NOESY
2822D 1H-1H NOESY
2922D 1H-19F HOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM potassium phosphate, 0.8 mM DNA/RNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL))-R(P*(A5O)P*(A5O)P*(UAR)P*(UAR))-D(P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'), 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
225 mM potassium phosphate, 100 mM sodium chloride, 0.8 mM DNA/RNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL))-R(P*(A5O)P*(A5O)P*(UAR)P*(UAR))-D(P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMpotassium phosphate-11
0.8 mMDNA/RNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL))-R(P*(A5O)P*(A5O)P*(UAR)P*(UAR))-D(P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')-21
100 mMsodium chloride-31
25 mMpotassium phosphate-42
100 mMsodium chloride-52
0.8 mMDNA/RNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL))-R(P*(A5O)P*(A5O)P*(UAR)P*(UAR))-D(P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')-62
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11007ambient 298 K
21007ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
SparkyGoddardpeak picking
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 194 / NOE intraresidue total count: 83 / NOE long range total count: 32 / NOE sequential total count: 61 / Hydrogen bond constraints total count: 64
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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