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- PDB-2k8z: Dimeric solution structure of the DNA loop d(TCGTTGCT) -

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Basic information

Entry
Database: PDB / ID: 2k8z
TitleDimeric solution structure of the DNA loop d(TCGTTGCT)
Components5'-D(*TP*CP*GP*TP*TP*GP*CP*T)-3'
KeywordsDNA / quadruplex / DNA-loop / minor groove tetrad
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsViladoms, J. / Escaja, N. / Frieden, M. / Gomez-Pinto, I. / Pedroso, E. / Gonzalez, C.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Self-association of short DNA loops through minor groove C:G:G:C tetrads.
Authors: Viladoms, J. / Escaja, N. / Frieden, M. / Gomez-Pinto, I. / Pedroso, E. / Gonzalez, C.
History
DepositionSep 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*CP*GP*TP*TP*GP*CP*T)-3'
B: 5'-D(*TP*CP*GP*TP*TP*GP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)4,8172
Polymers4,8172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

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


Mass: 2408.589 Da / Num. of mol.: 2 / 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 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

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Sample preparation

DetailsContents: 0.1-2.0 mM DNA (5'-D(*DTP*DCP*DGP*DTP*DTP*DGP*DCP*DT)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 10 mM magnesium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMDNA (5'-D(*DTP*DCP*DGP*DTP*DTP*DGP*DCP*DT)-3')0.1-2.01
25 mMsodium phosphate1
100 mMsodium chloride1
10 mMmagnesium chloride1
Sample conditionspH: 7 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DPXBrukerDPX8002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
DYANAGuntert, Braun and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
DYANAGuntert, Braun and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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