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- PDB-1db6: SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3... -

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Basic information

Entry
Database: PDB / ID: 1db6
TitleSOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE
ComponentsDNA
KeywordsDNA / APTAMER / ARGININE / ARGININAMIDE / SINGLE-STRAND / HAIRPIN / SELEX
Function / homologyARGININEAMIDE / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / Distance restraints were obtained from relaxation rate matrix calculations. Structures were calculated using simulated annealing, molecular dynamics
AuthorsRobertson, S.A. / Harada, K. / Frankel, A.D. / Wemmer, D.E.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure determination and binding kinetics of a DNA aptamer-argininamide complex.
Authors: Robertson, S.A. / Harada, K. / Frankel, A.D. / Wemmer, D.E.
#1: Journal: Embo J. / Year: 1995
Title: Identification of Two Novel Arginine Binding DNAs
Authors: Harada, K. / Frankel, A.D.
History
DepositionNov 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 1.4May 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9042
Polymers6,7291
Non-polymers1741
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 / 30structures with acceptable covalent geometry,structures with favorable non- bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #6fewest violations

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Components

#1: DNA chain DNA


Mass: 6729.329 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence is derived from in-vitro selection experiments. Sequences were chemically sythethesized.
#2: Chemical ChemComp-AAR / ARGININEAMIDE


Type: L-peptide linking / Mass: 174.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N5O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
2422D NOESY
NMR detailsText: Data were also collected for sequences containing 5-methyl cytosine substituted independently at positions 15 and 16, and for the sequence with inosine substituted at postion 14.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide99.99% D2O
21.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10-25 mM NaCl 6.2ambient 293 K
20-25 mM NaCl 6.2ambient 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
Bruker AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix950Molecular Simulations, Incdata analysis
MARDIGRAS3.2Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelliiterative matrix relaxation
Discover2.97Molecular Simulations, Increfinement
RefinementMethod: Distance restraints were obtained from relaxation rate matrix calculations. Structures were calculated using simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non- bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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