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- PDB-1ss7: Compensating bends in a 16 base-pair DNA oligomer containing a T3... -
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Basic information
Entry | Database: PDB / ID: 1ss7 | ||||||||||||||||||
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Title | Compensating bends in a 16 base-pair DNA oligomer containing a T3A3 segment | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B-DNA / double helix / Residual dipolar couplings | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / Restrained molecular dynamics | ![]() McAteer, K. / Aceves-Gaona, A. / Michalczyk, R. / Buchko, G.W. / Isern, N.G. / Silks, L.A. / Miller, J.H. / Kennedy, M.A. | ![]() ![]() Title: Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature Authors: McAteer, K. / Aceves-Gaona, A. / Michalczyk, R. / Buchko, G.W. / Isern, N.G. / Silks, L.A. / Miller, J.H. / Kennedy, M.A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 302.9 KB | Display | ![]() |
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PDB format | ![]() | 248.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 314.3 KB | Display | ![]() |
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Full document | ![]() | 478 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 19.7 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: 4898.191 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Heteronuclear dipolar couplings were measured in samples aligned with filamentous Pf1 bacteriophage |
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Sample preparation
Details | Contents: 1 mM DNA / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 400 mM NaCl, 40mM phosphate / pH: 7 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: Restrained molecular dynamics / Software ordinal: 1 Details: Structures are based on a total of 316 NOE, 90 torsion angle, and 6 distance restraints represented each W-C base-pair. For the RDC structures an additional 88 one-bond C-H and 14 one-bond N- ...Details: Structures are based on a total of 316 NOE, 90 torsion angle, and 6 distance restraints represented each W-C base-pair. For the RDC structures an additional 88 one-bond C-H and 14 one-bond N-H residual dipolar coupling restraints were used | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 45 / Conformers submitted total number: 15 |