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- PDB-2awv: NMR Structural Analysis of the dimer of 5MCCTCATCC -

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Basic information

Entry
Database: PDB / ID: 2awv
TitleNMR Structural Analysis of the dimer of 5MCCTCATCC
Components5'-D(*(MCY)P*CP*TP*CP*AP*CP*TP*CP*C)-3'
KeywordsDNA / i-motif / hemiprotonated CC+ pairs / dimer
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsCanalia, M. / Leroy, J.-L.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC).
Authors: Canalia, M. / Leroy, J.-L.
History
DepositionSep 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 29, 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*AP*CP*TP*CP*C)-3'
B: 5'-D(*(MCY)P*CP*TP*CP*AP*CP*TP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,0922
Polymers5,0922
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
RepresentativeModel #1lowest energy

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Components

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


Mass: 2545.773 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: chemicaly synthetized using the phosphoramidite method

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121E-COSY
1311H-31P COSY
NMR detailsText: This structure was determined using standard 2D homonuclear and heteronuclear techniques

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Sample preparation

DetailsContents: strand concentration: 0.1 to 10mM / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 1 Na / phosphate / pH: 4.5 / Pressure: 1 atm / Temperature: 278 K

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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
Felix97.2Hare D.processing
X-PLOR3.851Brunger Astructure solution
MOLMOL2.4Koradi,R.,Billeter, M and W trich, K.data analysis
X-PLOR3.851refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structure is based on 565 NOE-derived, distance constraints, 17 dihedral angle restraints, 20 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
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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