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Yorodumi- PDB-1ss7: Compensating bends in a 16 base-pair DNA oligomer containing a T3... -
+Open data
-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 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B-DNA / double helix / Residual dipolar couplings | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / Restrained molecular dynamics | Authors | McAteer, K. / Aceves-Gaona, A. / Michalczyk, R. / Buchko, G.W. / Isern, N.G. / Silks, L.A. / Miller, J.H. / Kennedy, M.A. | Citation | Journal: Biopolymers / Year: 2004 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ss7.cif.gz | 302.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ss7.ent.gz | 248.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ss7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/1ss7 ftp://data.pdbj.org/pub/pdb/validation_reports/ss/1ss7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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 |
-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 |