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- PDB-2n89: Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH -

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Basic information

Entry
Database: PDB / ID: 2n89
TitleTetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH
ComponentsDNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')
KeywordsDNA / 2'F-araC / i-motif / 2'F-ANA / Modified nucleotides
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsAbou-Assi, H. / Harkness, R.W. / Martin-Pintado, N. / Wilds, C.J. / Campos-Olivas, R. / Mittermaier, A.K. / Gonzalez, C. / Damha, M.J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Stabilization of i-motif structures by 2'-beta-fluorination of DNA.
Authors: Assi, H.A. / Harkness, R.W. / Martin-Pintado, N. / Wilds, C.J. / Campos-Olivas, R. / Mittermaier, A.K. / Gonzalez, C. / Damha, M.J.
History
DepositionOct 9, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')
B: DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')
C: DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')
D: DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,9654
Polymers6,9654
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 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain
DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')


Mass: 1741.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
2322D DQF-COSY
2422D 1H-1H TOCSY
2522D 1H-19F HOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-2.0 mM DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3'), 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.5-2.0 mM DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'), 10 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMDNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')-10.5-2.01
10 mMsodium chloride-21
mMDNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')-30.5-2.02
10 mMsodium chloride-42
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11051 atm278 K
21051 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmangeometry optimization
MOLMOLKoradi, Billeter and Wuthrichdata analysis
SparkyGoddardpeak picking
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: 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: 20 / Conformers submitted total number: 10

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