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- PDB-1ybr: Solution structure of the 5'E topology of the i-motif tetramer of... -

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Basic information

Entry
Database: PDB / ID: 1ybr
TitleSolution structure of the 5'E topology of the i-motif tetramer of d(CCCCAA)
Components5'-D(*CP*CP*CP*CP*AP*A)-3'
KeywordsDNA / i-motif / hemiprotonated cytidine / tetrahymena / telomer
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsEsmaili, N. / Leroy, J.-L.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats
Authors: Esmaili, N. / Leroy, J.-L.
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Source and taxonomy
Category: ndb_struct_conf_na / ndb_struct_na_base_pair_step ...ndb_struct_conf_na / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.twist / _pdbx_nmr_exptl_sample_conditions.temperature
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*CP*CP*AP*A)-3'
B: 5'-D(*CP*CP*CP*CP*AP*A)-3'
C: 5'-D(*CP*CP*CP*CP*AP*A)-3'
D: 5'-D(*CP*CP*CP*CP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)6,9534
Polymers6,9534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5040 Å2
ΔGint11 kcal/mol
Surface area2260 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

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Components

#1: DNA chain
5'-D(*CP*CP*CP*CP*AP*A)-3'


Mass: 1738.183 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: i-motif with a distinct topology / 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 NOESY
1212D TOCSY
131HMBC
NMR detailsText: Standard 2D methods

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Sample preparation

DetailsContents: pH 4.5 / Solvent system: H2O/D2O
Sample conditionsIonic strength: no added salt / pH: 4.5 / Pressure: normal / Temperature: 273 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.T.structure solution
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 352 NOE-derived distances restraints and 12 H-bonding restraints derived from proton exchange measurements
NMR representativeSelection criteria: fewest violations
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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