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- PDB-1s74: 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: 1s74 | ||||||
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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 | ![]() | 22.6 KB | Display | ![]() |
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PDB format | ![]() | 14.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 251.9 KB | Display | ![]() |
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Full document | ![]() | 251.7 KB | Display | |
Data in XML | ![]() | 1.9 KB | Display | |
Data in CIF | ![]() | 2.1 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. THIS STRUCTURE WAS FURTHER REFINED BY RMD IN VACUO WITH AN ADDITIONAL 25 C-H RESIDUAL DIPOLAR COUPLINGS, FOLLOWED BY REM. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||
NMR ensemble | Conformers calculated total number: 10 / Conformers submitted total number: 1 |