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- PDB-2k97: Dimeric solution structure of the cyclic octamer d(pCGCTCCGT) -

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Basic information

Entry
Database: PDB / ID: 2k97
TitleDimeric solution structure of the cyclic octamer d(pCGCTCCGT)
Components5'-D(P*CP*GP*CP*TP*CP*CP*GP*T)-3'
KeywordsDNA / quadruplex / DNA-loop / minor groove tetrad
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsSelf-association of the cyclic octamer d(pCGCTCCGT) gives rise to a quadruplex stabilized by minor ...Self-association of the cyclic octamer d(pCGCTCCGT) gives rise to a quadruplex stabilized by minor groove tetrads
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 30, 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 / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4May 8, 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: 5'-D(P*CP*GP*CP*TP*CP*CP*GP*T)-3'
B: 5'-D(P*CP*GP*CP*TP*CP*CP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)4,7572
Polymers4,7572
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(P*CP*GP*CP*TP*CP*CP*GP*T)-3'


Mass: 2378.567 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Self-association of the cyclic octamer d(pCGCTCCGT) gives rise to a quadruplex stabilized by minor groove tetrads
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

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Sample preparation

DetailsContents: 0.1-4.0 mM DNA (cyclic D(*DCP*DGP*DCP*DTP*DCP*DCP*DGP*DTP)), 25 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMDNA (cyclic D(*DCP*DGP*DCP*DTP*DCP*DCP*DGP*DTP))0.1-4.01
25 mMsodium phosphate1
100 mMsodium chloride1
Sample conditionspH: 7 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX8002

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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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