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- PDB-1s88: NMR structure of a DNA duplex with two INA nucleotides inserted o... -

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Basic information

Entry
Database: PDB / ID: 1s88
TitleNMR structure of a DNA duplex with two INA nucleotides inserted opposite each other, dCTCAACXCAAGCT:dAGCTTGXGTTGAG
Components
  • 5'-D(*AP*GP*CP*TP*TP*GP*(2DM)P*GP*TP*TP*GP*AP*G)-3'
  • 5'-D(*CP*TP*CP*AP*AP*CP*(2DM)P*CP*AP*AP*GP*CP*T)-3'
KeywordsDNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / restraint molecular dynamics
AuthorsNielsen, C.B. / Petersen, M. / Pedersen, E.B. / Hansen, P.E. / Christensen, U.B.
CitationJournal: Bioconjug.Chem. / Year: 2004
Title: NMR structure determination of a modified DNA oligonucleotide containing a new intercalating nucleic acid.
Authors: Nielsen, C.B. / Petersen, M. / Pedersen, E.B. / Hansen, P.E. / Christensen, U.B.
History
DepositionJan 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: 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: 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 22, 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: 5'-D(*CP*TP*CP*AP*AP*CP*(2DM)P*CP*AP*AP*GP*CP*T)-3'
B: 5'-D(*AP*GP*CP*TP*TP*GP*(2DM)P*GP*TP*TP*GP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)8,0612
Polymers8,0612
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 / 40structures with the lowest energy
Representative

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Components

#1: DNA chain 5'-D(*CP*TP*CP*AP*AP*CP*(2DM)P*CP*AP*AP*GP*CP*T)-3'


Mass: 3959.690 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*GP*CP*TP*TP*GP*(2DM)P*GP*TP*TP*GP*AP*G)-3'


Mass: 4101.758 Da / Num. of mol.: 1 / 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
131DQF-COSY
1422D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.9mM DNA, 10mM sodium phosphate buffer, 100mM NaCl, 0.05mM EDTA, 100% D2O100% D2O
21.9mM DNA, 10mM sodium phosphate buffer, 100mM NaCl, 0.05mM EDTA, 90% H2O 10% D2090% H2O 10% D20
Sample conditionsIonic strength: 100 mM / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber6Caseiterative matrix relaxation
Felix98MSI, San Diego, CAprocessing
RefinementMethod: restraint molecular dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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