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Yorodumi- PDB-1naj: High resolution NMR Structure Of DNA Dodecamer Determined In Aque... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1naj | ||||||||||||||||||
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Title | High resolution NMR Structure Of DNA Dodecamer Determined In Aqueous Dilute Liquid Crystalline Phase | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Dickerson Dodecamer | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS | Authors | Wu, Z. / Delaglio, F. / Tjandra, N. / Zhurkin, V. / Bax, A. | Citation | Journal: J.Biomol.Nmr / Year: 2003 | Title: Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and (31)P chemical shift anisotropy. Authors: Wu, Z. / Delaglio, F. / Tjandra, N. / Zhurkin, V.B. / Bax, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1naj.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1naj.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 1naj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/1naj ftp://data.pdbj.org/pub/pdb/validation_reports/na/1naj | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 3663.392 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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-Sample preparation
Details |
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Sample conditions | Ionic strength: 40mM / pH: 7.0 / Pressure: 1 atm / Temperature: 308 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-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: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1 Details: THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 32 HYDROGEN BOND, AND 24 DIHEDRAL RESTRAINTS; AS WELL AS 262 CH AND 16 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS, 200 APPROXIMATE PROTON-PROTON ...Details: THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 32 HYDROGEN BOND, AND 24 DIHEDRAL RESTRAINTS; AS WELL AS 262 CH AND 16 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS, 200 APPROXIMATE PROTON-PROTON DIPOLAR COUPLINGS, 300 quantitative proton-proton dipolar restraints, 22 31P-1H dipolar couplings, and 22 31P chemical shift anisotropy restraints. THE COORDINATE OF THE ALIGNMENT TENSOR IS DEFINED BY molecule 500 and 501. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 5 |