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Yorodumi- PDB-214d: THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 214d | ||||||
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Title | THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT | ||||||
Components |
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Keywords | DNA / DOUBLE HELIX | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION | ||||||
Authors | Gotfredsen, C.H. / Spielmann, H.P. / Wengel, J. / Jacobsen, J.P. | ||||||
Citation | Journal: Bioconjug.Chem. / Year: 1996 Title: Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. Authors: Gotfredsen, C.H. / Spielmann, H.P. / Wengel, J. / Jacobsen, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 214d.cif.gz | 541.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb214d.ent.gz | 470.5 KB | Display | PDB format |
PDBx/mmJSON format | 214d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/14/214d ftp://data.pdbj.org/pub/pdb/validation_reports/14/214d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3318.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID |
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#2: DNA chain | Mass: 3419.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
Software | Name: AMBER / Classification: refinement | |||||||||
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NMR software |
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Refinement | Method: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1 Details: REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY ...Details: REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY SPECTRA DURING THESE CALCULATIONS HAVE BEEN EMPLOYED (H.LIU, H.P.SPIELMANN, D.E.WEMMER, AND T.L.JAMES (1995) IN PREPARATION). THE NOE-DERIVED DISTANCE RESTRAINTS WERE APPLIED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WITH AMBER FORCEFIELD POTENTIALS AS IMPLEMENTED IN DISCOVER. THE ROOT-MEAN-SQUARE (RMS) DEVIATION OF THE COORDINATES FOR THE FORTY STRUCTURES OF THE DUPLEX WAS 0.82 ANGSTROMS. | |||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 40 / Conformers submitted total number: 40 |