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- PDB-2jt7: NMR solution structure of the 4:1 distamycin A/[d(TGGGGT)]4 complex -

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Basic information

Entry
Database: PDB / ID: 2jt7
TitleNMR solution structure of the 4:1 distamycin A/[d(TGGGGT)]4 complex
ComponentsDNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')
KeywordsDNA / quadruplex / distamycin A / TGGGGT / complex / telomere
Function / homologyDISTAMYCIN A / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsMartino, L. / Virno, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4
Authors: Martino, L. / Virno, A. / Pagano, B. / Virgilio, A. / Di Micco, S. / Galeone, A. / Giancola, C. / Bifulco, G. / Mayol, L. / Randazzo, A.
History
DepositionJul 20, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 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: DNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')
B: DNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')
E: DNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')
F: DNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4478
Polymers7,5214
Non-polymers1,9264
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain
DNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')


Mass: 1880.251 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-DMY / DISTAMYCIN A / DISTAMYCIN / STALLIMYCIN


Mass: 481.508 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H27N9O4 / Comment: antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
1222D 1H-1H TOCSY
1322D 1H-1H COSY
1422D 1H-1H NOESY
2512D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM DNA, 90% H2O/10% D2O90% H2O/10% D2O
22 mM DNA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMDNA (5'-D(*TP*GP*GP*GP*GP*T)-3')1
2 mMDNA (5'-D(*TP*GP*GP*GP*GP*T)-3')2
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DiscoverfAccelrys Software Inc.structure solution
FelixAccelrys Software Inc.chemical shift assignment
DiscoverfAccelrys Software Inc.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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