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- PDB-1s0t: Solution structure of a DNA duplex containing an alpha-anomeric a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s0t | ||||||
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Title | Solution structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate recognition by endonuclease IV | ||||||
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![]() | DNA / DNA double helix with enlarged miner groove and helical kink | ||||||
Function / homology | DNA![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics molecular dynamics | ||||||
Model type details | minimized average | ||||||
![]() | Aramini, J.M. / Cleaver, S.H. / Pon, R.T. / Cunningham, R.P. / Germann, M.W. | ||||||
![]() | ![]() Title: Solution Structure of a DNA Duplex Containing an alpha-Anomeric Adenosine: Insights into Substrate Recognition by Endonuclease IV. Authors: Aramini, J.M. / Cleaver, S.H. / Pon, R.T. / Cunningham, R.P. / Germann, M.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.2 KB | Display | ![]() |
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PDB format | ![]() | 14.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 240.4 KB | Display | ![]() |
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Full document | ![]() | 240.1 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 1.9 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: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The core of the sequence corresponds to the recognition site of E. coli endonuclease IV |
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#2: DNA chain | Mass: 3061.003 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: For non-exchangeable protons, NOESY experiments in D2O were performed with 10s relaxation delays and mixing times of 75ms, 150ms and 250 ms. For exchangeable protons, a WATERGATE NOESY was ...Text: For non-exchangeable protons, NOESY experiments in D2O were performed with 10s relaxation delays and mixing times of 75ms, 150ms and 250 ms. For exchangeable protons, a WATERGATE NOESY was performed with a relaxation delay of 4s and 150ms mixing time. |
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Sample preparation
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics molecular dynamics / Software ordinal: 1 Details: The structure is based on a total of 502 restraints: 284 distance restraints, 80 endocyclic torsion angle restraints, 50 Watson-Crick distance and angle restraints, and 88 backbone torsion ...Details: The structure is based on a total of 502 restraints: 284 distance restraints, 80 endocyclic torsion angle restraints, 50 Watson-Crick distance and angle restraints, and 88 backbone torsion angle restraints. The alphaA duplex structure was elucidated by a combination of DYANA and rMD/rEM in AMBER. All calculations were performed in vacuo. The final structure deposited here was obtained by coordinate averaging the final ensemble of 10 rMD/rEM structures followed by restrained energy minimization. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||
NMR ensemble | Conformers calculated total number: 10 / Conformers submitted total number: 1 |