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Yorodumi- PDB-148d: THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN BINDING DNA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 148d | ||||||||||||||||||
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Title | THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN BINDING DNA APTAMER D(GGTTGGTGTGGTTGG) | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / SIMULATED ANNEALING, MATRIX RELAXATION | Authors | Schultze, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 148d.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb148d.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 148d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 148d_validation.pdf.gz | 305.2 KB | Display | wwPDB validaton report |
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Full document | 148d_full_validation.pdf.gz | 371 KB | Display | |
Data in XML | 148d_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 148d_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/48/148d ftp://data.pdbj.org/pub/pdb/validation_reports/48/148d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Details | Solvent system: H2O/D2O |
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Sample | Conc.: .0023 M / Component: POTASSIUM CHLORIDE |
Sample conditions | Ionic strength: 0.11M / pH: 6.1 / Temperature units: K |
Crystal grow | *PLUS Method: other / Details: NMR |
-Processing
Software |
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Refinement | Method: 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 representative | Selection criteria: closest to the average | ||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 12 |