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- PDB-2k69: NMR solution structure of modified DNA containing imidazole nucle... -

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Basic information

Entry
Database: PDB / ID: 2k69
TitleNMR solution structure of modified DNA containing imidazole nucleosides at basic pH
ComponentsDNA (5'-D(*DTP*DTP*DAP*DAP*DTP*DTP*DTP*(D33)P*(D33)P*(D33)P*DAP*DAP*DAP*DTP*DTP*DAP*DA)-3')
KeywordsDNA / DNA 17-mer / hairpin / artificial nucleobase / imidazole nucleoside / shifted pKa
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsJohannsen, S. / Boehme, D. / Duepre, N. / Mueller, J. / Sigel, R.K.O.
CitationJournal: To be Published
Title: Solution structure at different pHs of a DNA hairpin containing artificial nucleotides
Authors: Johannsen, S. / Boehme, D. / Duepre, N. / Mueller, J. / Sigel, R.K.O.
History
DepositionJul 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*DTP*DTP*DAP*DAP*DTP*DTP*DTP*(D33)P*(D33)P*(D33)P*DAP*DAP*DAP*DTP*DTP*DAP*DA)-3')


Theoretical massNumber of molelcules
Total (without water)5,0151
Polymers5,0151
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*DTP*DTP*DAP*DAP*DTP*DTP*DTP*(D33)P*(D33)P*(D33)P*DAP*DAP*DAP*DTP*DTP*DAP*DA)-3')


Mass: 5015.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DID_DNA_17-mer

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-13C HSQC
2422D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM DID DNA 17-mer, 120 mM sodium perchlorate, 100% D2O100% D2O
20.5 mM DID DNA 17-mer, 120 mM sodium perchlorate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMDID DNA 17-mer1
120 mMsodium perchlorate1
0.5 mMDID DNA 17-mer2
120 mMsodium perchlorate2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1120mM 10.2ambient 298 K
2120mM 10.2ambient 278 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3, 2.0, 2.1Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
DYANA1.5Guntert, Braun and Wuthrichstructure solution
X-PLOR NIH2.15Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 411 / NOE intraresidue total count: 164 / NOE long range total count: 28 / NOE medium range total count: 11 / NOE sequential total count: 208
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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