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- PDB-2idn: NMR structure of a new modified Thrombin Binding Aptamer containi... -

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Basic information

Entry
Database: PDB / ID: 2idn
TitleNMR structure of a new modified Thrombin Binding Aptamer containing a 5'-5' inversion of polarity site
Components3'-D(P*GP*G*T)-5'-5'-D(P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'
KeywordsDNA / Inversion of polarity / TBA / anticoagulant / quadruplex / 5'-5'
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsRandazzo, A. / Martino, L. / Virno, A. / Mayol, L. / Giancola, C.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: A new modified thrombin binding aptamer containing a 5'-5' inversion of polarity site.
Authors: Martino, L. / Virno, A. / Randazzo, A. / Virgilio, A. / Esposito, V. / Giancola, C. / Bucci, M. / Cirino, G. / Mayol, L.
History
DepositionSep 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage / 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The phosphate group in T3 is missing due to the 5'-3' inversion of this strand.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3'-D(P*GP*G*T)-5'-5'-D(P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)4,7431
Polymers4,7431
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)7 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The original sequence (the one without inversion of polarity) has been selected in the SELEX process

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
2311H-15N HSQC
1422D TOCSY
152PE-COSY
1622D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques, and by using a 1H-15N HSQC performed on the unlabeled molecule

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM phosphate buffer K, 70 mM KCl, 0.2 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
220 mM phosphate buffer K, 70 mM KCl, 0.2 mM EDTA, D2OD2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17 ambient 298 K
27 ambient 278 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Unity InovaVarianUnity Inova7001
Varian Unity InovaVarianUnity Inova5002

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Processing

NMR software
NameVersionDeveloperClassification
Insight II2005Accelrysdata analysis
DiscoverAccelrysrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 288 restraints, 198 are NOE-derived distance constraints, 54 dihedral angle restraints, 36 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 7

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