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- PDB-1kkv: NMR Solution Structure of d(CCACGCGTGG)2, parent to G-T mismatch ... -

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Entry
Database: PDB / ID: 1kkv
TitleNMR Solution Structure of d(CCACGCGTGG)2, parent to G-T mismatch structure
Components5'-D(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-3'
KeywordsDNA / g-t mismatch / dynamics / spin relaxation / order parameter / helical parameter / sequence dependent structure / sequence dependent dynamics
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsIsaacs, R.J. / Spielmann, H.P.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics.
Authors: Isaacs, R.J. / Rayens, W.S. / Spielmann, H.P.
History
DepositionDec 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-3'
B: 5'-D(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
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)20 / 20all calculated structures submitted, back calculated data agree with experimental NOESY spectrum
RepresentativeModel #16closest to the average

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Components

#1: DNA chain 5'-D(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-3'


Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized from phosphoramadites on solid support

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 4 mM double strand DNA / Solvent system: 99.96% D2O
Sample conditionsIonic strength: 200 mM NaCl, 20 mM NaPO4, 10 mM NaN3, 0.1 mM EDTA
pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6bvarian, inc.collection
Felix98accelrysdata analysis
MARDIGRAS1James, T.L.iterative matrix relaxation
Discover2.98accelrysstructure solution
Discover2.98accelrysrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted, back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 20 / Conformers submitted total number: 20

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