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Yorodumi- PDB-1ii1: Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ii1 | ||||||||||||||||||
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Title | Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Uracil / Hairpin DNA / Hairpin loop / Double helix / UDG-Uracil interaction | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / restrained molecular dynamics, energy minimization | Authors | Ghosh, M. / Rumpal, N. / Varshney, U. / Chary, K.V. | Citation | Journal: Eur.J.Biochem. / Year: 2002 | Title: Structural basis for poor uracil excision from hairpin DNA. An NMR study. Authors: Ghosh, M. / Rumpal, N. / Varshney, U. / Chary, K.V. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ii1.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ii1.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ii1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/1ii1 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/1ii1 | HTTPS FTP |
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-Related structure data
Related structure data | 1idxC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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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: 5483.537 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Custom made Ransom Hill Biosciences, Inc., Ramona CA (USA) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using 2D homonuclear techniques |
-Sample preparation
Details |
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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: restrained molecular dynamics, energy minimization / Software ordinal: 1 Details: The structures are based on total of 227 restraints, 143 are NOE-derived distance constraints, 64 dihedral angle restraints, 10 distance restraints from hydrogen bonds. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations,lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |