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- PDB-2mjx: Solution NMR structure of a mismatch DNA -

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Basic information

Entry
Database: PDB / ID: 2mjx
TitleSolution NMR structure of a mismatch DNA
Components
  • DNA (5'-D(*CP*GP*CP*GP*TP*AP*CP*GP*AP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*CP*AP*TP*GP*CP*TP*AP*CP*GP*CP*G)-3')
KeywordsDNA / mismatch DNA / G-G mismatch
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsGhosh, A. / Kumar, K.R. / Bhunia, A. / Chatterjee, S.
CitationJournal: Chemmedchem / Year: 2014
Title: Double GC:GC mismatch in dsDNA enhances local dynamics retaining the DNA footprint: a high-resolution NMR study
Authors: Ghosh, A. / Kar, R.K. / Krishnamoorthy, J. / Chatterjee, S. / Bhunia, A.
History
DepositionJan 21, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,5642
Polymers8,5642
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)8 / 8structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4281.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*AP*CP*GP*AP*TP*GP*CP*GP*C)-3')


Mass: 4281.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM DNA (28-MER)-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: DNA (28-MER)-1
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmangeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 27 / NA beta-angle constraints total count: 27 / NA chi-angle constraints total count: 27 / NA delta-angle constraints total count: 28 / NA epsilon-angle constraints total count: 27 / NA gamma-angle constraints total count: 28 / NA sugar pucker constraints total count: 28
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 8 / Conformers submitted total number: 8 / Representative conformer: 1

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