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- PDB-1q2t: Solution structure of d(5mCCTCTCC)4 -

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Basic information

Entry
Database: PDB / ID: 1q2t
TitleSolution structure of d(5mCCTCTCC)4
Components5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3'
KeywordsDNA / DNA solution structure / i-motif / protonated cytidine / hemiprotonated base-pairs
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsLeroy, J.-L.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: T.T pair intercalation and duplex inter-conversion within i-motif tetramers
Authors: Leroy, J.-L.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.
Authors: Nonin, S. / Leroy, J.-L.
History
DepositionJul 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 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: 5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3'
B: 5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3'
C: 5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3'
D: 5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,7744
Polymers7,7744
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)1 / 10back calculated data agree with experimental NOESY spectrum
Representative

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Components

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


Mass: 1943.384 Da / Num. of mol.: 4 / 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 NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 10mM DNA strand / Solvent system: H2O 90%, D2O 10%
Sample conditionsIonic strength: No added counter-ions / pH: 4.4 / Pressure: ambient / Temperature: 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structure is based on a total of 172 restraints. 30 base-pairing restraints from hydrogen bonds, 78 NOE-distance restraints and 36 repulsive restraints reflecting the absence of NOE
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 1

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