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- PDB-148d: THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN BINDING DNA ... -

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Basic information

Entry
Database: PDB / ID: 148d
TitleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN BINDING DNA APTAMER D(GGTTGGTGTGGTTGG)
ComponentsDNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
KeywordsDNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, MATRIX RELAXATION
AuthorsSchultze, P. / Macaya, R.F. / Feigon, J.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG).
Authors: Schultze, P. / Macaya, R.F. / Feigon, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Thrombin-Binding DNA Aptamer Forms a Unimolecular Quadruplex Structure in Solution
Authors: Macaya, R.F. / Schultze, P. / Smith, F.W. / Roe, J.A. / Feigon, J.
History
DepositionNov 15, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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 (5'-D(*GP*GP*TP*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)12 / 20target function
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*GP*GP*TP*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: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsSolvent system: H2O/D2O
SampleConc.: .0023 M / Component: POTASSIUM CHLORIDE
Sample conditionsIonic strength: 0.11M / pH: 6.1 / Temperature units: K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod: SIMULATED ANNEALING, MATRIX RELAXATION / Software ordinal: 1
Details: STEP (1) SUBSTRUCTURE EMBEDDING ON 20 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY SIMULATED ANNEALING (20 STRUCTURES) STEP (3) SIMULATED ANNEALING AND ENERGY MINIMIZATION (20 ...Details: STEP (1) SUBSTRUCTURE EMBEDDING ON 20 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY SIMULATED ANNEALING (20 STRUCTURES) STEP (3) SIMULATED ANNEALING AND ENERGY MINIMIZATION (20 STRUCTURES) STEP (4) RELAXATION MATRIX REFINEMENT ON THE BEST 6 OF 20 STRUCTURES THIS PROCEDURE WAS CARRIED OUT SEPARATELY WITH DISTANCE RESTRAINTS ENFORCING HYDROGEN BONDING BETWEEN T4 AND T13 INVOLVING O2 ATOMS IN ONE CASE (MODELS 1-6) AND O4 ATOMS IN THE OTHER (MODELS 7-12). ALL MODELS WERE SUPERIMPOSED ON MODEL 1, USING ALL NON-HYDROGEN ATOMS OF G1, G2, G5, G6, G10, G11, G14, G15; I.E., ALL G RESIDUES PARTICIPATING IN TETRAD FORMATION.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 12

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