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Open data
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Basic information
Entry | Database: PDB / ID: 1g80 | ||||||||||||||||||
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Title | NMR SOLUTION STRUCTURE OF D(GCGTACGC)2 | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / PSORALEN / HMT / C13 DYNAMICS / CONFORMATIONAL EXCHANGE / PHOSPHATE CONFORMATION / DEOXYRIBOSE CONFORMATION / HELICAL PARAMETER / ORDER PARAMETER | Function / homology | DNA | ![]() Method | SOLUTION 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. | ![]() Isaacs, R.J. / Spielmann, H.P. | ![]() ![]() 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: ![]() Title: Dynamics in Psoralen-Damaged DNA by 1H-Detected Natural Abundance 13C NMR Spectroscopy Authors: Spielmann, H.P. #2: ![]() Title: Solution structures of psoralen monoadducted and cross-linked DNA oligomers by NMR spectroscopy and restrained molecular dynamics. Authors: Spielmann, H.P. / Dwyer, T.J. / Hearst, J.E. / Wemmer, D.E. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.6 KB | Display | ![]() |
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PDB format | ![]() | 168 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 311.2 KB | Display | ![]() |
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Full document | ![]() | 432.1 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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: phosphoramadites on solid support |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
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Sample preparation
Details | Contents: 4 mM DNA duplex / Solvent system: 99.9% D2O |
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Sample conditions | Ionic strength: NaCl(100mM), PO4-(20mM), NaN3(10mM), EDTA(0.1mM) pH: 7.0 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | 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 ...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 524 restraints, 502 are NOE-derived distance constraints and 22 distance restraints from hydrogen bonds. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest pairwise rmsd from other conformers | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 20 / Conformers submitted total number: 20 |