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Yorodumi- PDB-108d: THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 108d | ||||||||||||||||||
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Title | THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / FLUORESCENT BIS INTERCALATOR / TOTO / BIS-THIAZOLE ORANGE | Function / homology | Chem-TOT / DNA | Function and homology information Method | SOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION | Authors | Spielmann, H.P. / Wemmer, D.E. / Jacobsen, J.P. | Citation | Journal: Biochemistry / Year: 1995 | Title: Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy. Authors: Spielmann, H.P. / Wemmer, D.E. / Jacobsen, J.P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 108d.cif.gz | 481.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb108d.ent.gz | 402.9 KB | Display | PDB format |
PDBx/mmJSON format | 108d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/08/108d ftp://data.pdbj.org/pub/pdb/validation_reports/08/108d | HTTPS FTP |
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-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: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID #2: Chemical | ChemComp-TOT / | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Crystal grow | *PLUS Method: other |
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-Processing
Software | Name: AMBER / Classification: refinement | |||||||||
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NMR software |
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Refinement | Method: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1 Details: REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY ...Details: REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY SPECTRA DURING THESE CALCULATIONS HAVE BEEN EMPLOYED (LIU, H., SPIELMANN, H.P., WEMMER, D.E., & JAMES, T.L. (1995) IN PREPARATION). THE NOE DERIVED DISTANCE RESTRAINTS WERE APPLIED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS USING THE PROGRAM DISCOVER VERSION 2.9.5 WITH MODIFIED AMBER FORCE-FIELD POTENTIALS AS IMPLEMENTED IN DISCOVER. THE ROOT-MEAN-SQUARE (RMS) DEVIATION OF THE COORDINATES FOR THE FORTY STRUCTURES OF THE COMPLEX WAS 1.4 ANGSTROMS (INCLUDING THE DISORDERED TERMINAL DNA RESIDUES). THE COMPLEX EXHIBITS TWO-FOLD SPECTROSCOPIC SYMMETRY, BUT NO SYMMETRY WAS IMPOSED DURING THE REFINEMENT. DEVIATIONS FROM IDEAL TWO-FOLD SYMMETRY REFLECT THE UNCERTAINTY IN THE NMR DATA. THE 40 STRUCTURES ARE BASED ON 362 INTERPROTON DISTANCE RESTRAINTS FROM NOE MEASUREMENTS, 22 HYDROGEN BOND DISTANCE RESTRAINTS, AND 48 RESTRAINTS TO ENFORCE CHIRALITY IN THE DEOXYRIBOSE RESIDUES. THE FIRST 20 STRUCTURES WERE GENERATED FROM B-FORM DNA STARTING COORDINATES, AND THE SECOND 20 STRUCTURES WERE GENERATED FROM A-FORM DNA STARTING COORDINATES. | |||||||||
NMR ensemble | Conformers submitted total number: 40 |