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- PDB-1g7z: NMR SOLUTION STRUCTURE OF D(CGCTAGCG)2 -

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Basic information

Entry
Database: PDB / ID: 1g7z
TitleNMR SOLUTION STRUCTURE OF D(CGCTAGCG)2
Components5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3'
KeywordsDNA / TOTO / C13 DYNAMICS / CONFORMATIONAL EXCHANGE / PHOSPHATE CONFORMATION / DEOXYRIBOSE CONFORMATION / HELICAL PARAMETER / ORDER PARAMETER
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / The RANDMARDI procedure of the complete relaxation matrix analysis method, MARDIGRAS, was used to calculate interproton distance bounds from the integrated NOESY cross-peak intensities. These distance bounds were then used as restraints in an RMD procedure to yield 20 structures.
AuthorsIsaacs, R.J. / Spielmann, H.P.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters ...Title: Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters implies conformational coupling in dinucleotide units.
Authors: Isaacs, R.J. / Spielmann, H.P.
#1: Journal: Biochemistry / Year: 1998
Title: Dynamics of a Bis-intercalator DNA Complex by 1H-Detected Natural Abundance 13C NMR Spectroscopy
Authors: Spielmann, H.P.
#2: 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
DepositionNov 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: 5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
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)20 / 20back calculated data agree with experimental NOESY spectrum
RepresentativeModel #12lowest pairwise rmsd from other conformers

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Components

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


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phosphoramadites on solid support

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 4 mM DNA duplex / Solvent system: 99.96% D2O
Sample conditionsIonic strength: NaCl(100mM),PO4-(20mM),NaN3(10mM),EDTA(0.1mM)
pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVariancollection
Felix98MSIdata analysis
MARDIGRAS3.2James, TLiterative matrix relaxation
Discover2.98MSIstructure solution
Discover2.98MSIrefinement
RefinementMethod: The RANDMARDI procedure of the complete relaxation matrix analysis method, MARDIGRAS, was used to calculate interproton distance bounds from the integrated NOESY cross-peak intensities. These ...Method: The RANDMARDI procedure of the complete relaxation matrix analysis method, MARDIGRAS, was used to calculate interproton distance bounds from the integrated NOESY cross-peak intensities. These distance bounds were then used as restraints in an RMD procedure to yield 20 structures.
Software ordinal: 1
Details: The structures are based on a total of 540 restraints, 518 are NOE-derived distance constraints and 22 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest pairwise rmsd from other conformers
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 20 / Conformers submitted total number: 20

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