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- PDB-2kk5: High Fidelity Base Pairing at the 3'-Terminus -

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Basic information

Entry
Database: PDB / ID: 2kk5
TitleHigh Fidelity Base Pairing at the 3'-Terminus
Components5'-D(*AP*CP*GP*CP*GP*(2AU))-3'
KeywordsDNA / Anthraquinone-linked DNA
Function / homology9,10-dioxo-9,10-dihydroanthracene-2-carboxamide / DNA
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsPatra, A. / Richert, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: High fidelity base pairing at the 3'-terminus.
Authors: Patra, A. / Richert, C.
History
DepositionJun 15, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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(*AP*CP*GP*CP*GP*(2AU))-3'
B: 5'-D(*AP*CP*GP*CP*GP*(2AU))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1234
Polymers3,6202
Non-polymers5022
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*AP*CP*GP*CP*GP*(2AU))-3'


Mass: 1810.206 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-AQC / 9,10-dioxo-9,10-dihydroanthracene-2-carboxamide


Mass: 251.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H9NO3

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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: 2 mM Anthraquinon capped DNA duplex, 100% D2O, 90% H2O/10% D2O
Solvent system: 100% D2O, 90% H2O/10% D2O
SampleConc.: 2 mM / Component: Anthraquinon capped DNA duplex-1
Sample conditionsIonic strength: 0.15 / pH: 7 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 3

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