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- PDB-2e4i: Human Telomeric DNA mixed-parallel/antiparallel quadruplex under ... -

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Basic information

Entry
Database: PDB / ID: 2e4i
TitleHuman Telomeric DNA mixed-parallel/antiparallel quadruplex under Physiological Ionic Conditions Stabilized by Proper Incorporation of 8-Bromoguanosines
ComponentsDNA (5'-D(*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*(BGM)P*(BGM)P*DGP*DTP*DTP*DAP*(BGM)P*DGP*DG)-3')
KeywordsDNA / telomere / quadruplex / mixed-parallel/antiparallel
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsMatsugami, A. / Xu, Y. / Noguchi, Y. / Sugiyama, H. / Katahira, M.
CitationJournal: Febs J. / Year: 2007
Title: Structure of a human telomeric DNA sequence stabilized by 8-bromoguanosine substitutions, as determined by NMR in a K+ solution
Authors: Matsugami, A. / Xu, Y. / Noguchi, Y. / Sugiyama, H. / Katahira, M.
History
DepositionDec 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*(BGM)P*(BGM)P*DGP*DTP*DTP*DAP*(BGM)P*DGP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)7,3781
Polymers7,3781
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)1 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*(BGM)P*(BGM)P*DGP*DTP*DTP*DAP*(BGM)P*DGP*DG)-3')


Mass: 7377.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human Telomeric DNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
153JR-HMBC
16313C-HSQC
171H, P HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS, 100% D2O100% D2O
20.6mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS, 95% H2O, 5% D2O95% H2O/5% D2O
31.3mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 110mM Potassium Ion / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4F. Delaglioprocessing
XwinNMR3.5Brukerprocessing
PIPP4.3.2D. Garrettdata analysis
Spaky3.112T.D. Goddarddata analysis
X-PLOR3.851A.T. Brungerstructure solution
X-PLOR3.851A.T. Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 752 restraints, 582 are NOE-derived distance constraints, 110 dihedral angle restraints,48 distance restraints from hydrogen bonds, 12 planarity ...Details: the structures are based on a total of 752 restraints, 582 are NOE-derived distance constraints, 110 dihedral angle restraints,48 distance restraints from hydrogen bonds, 12 planarity restraints for tetrad planes.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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