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- PDB-108d: THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS ... -

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Entry
Database: PDB / ID: 108d
TitleTHE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY
ComponentsDNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
KeywordsDNA / FLUORESCENT BIS INTERCALATOR / TOTO / BIS-THIAZOLE ORANGE
Function / homologyChem-TOT / DNA
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsSpielmann, H.P. / Wemmer, D.E. / Jacobsen, J.P.
CitationJournal: 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
DepositionJan 31, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6503
Polymers4,8552
Non-polymers7951
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / -
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: Chemical ChemComp-TOT / 1,1-(4,4,8,8-TETRAMETHYL-4,8-DIAZAUNDECAMETHYLENE)-BIS-4-3-METHYL-2,3-DIHYDRO-(BENZO-1,3-THIAZOLE)-2-METHYLIDENE)-QUINOLINIUM / BIS-THIAZOLE ORANGE


Mass: 795.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H58N6S2 / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionClassification
MARDIGRASrefinement
Discover2.9.5refinement
RefinementMethod: 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 ensembleConformers submitted total number: 40

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