[English] 日本語
Yorodumi- PDB-1p96: Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p96 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA | ||||||
Components |
| ||||||
Keywords | DNA / Wedge-shaped synthetic drug-bulged DNA complex | ||||||
Function / homology | Chem-DDI / DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / distance geometry sinulated annealing | ||||||
Authors | Hwang, G.S. / Jones, G.B. / Goldberg, I.H. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA Authors: Hwang, G.S. / Jones, G.B. / Goldberg, I.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1p96.cif.gz | 178.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1p96.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 1p96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p96 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p96 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 4265.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by DNA synthesizer. |
---|---|
#2: DNA chain | Mass: 3694.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by DNA synthesizer. |
#3: Chemical | ChemComp-DDI / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||
NMR details | Text: This structure was determined using 2D homonuclear and heteronuclear techniques. |
-Sample preparation
Details | Contents: 1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20 Solvent system: 90% H20/10% D20; 99.96% D20 |
---|---|
Sample conditions | Ionic strength: 0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA pH: 6.5 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
|
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: distance geometry sinulated annealing / Software ordinal: 1 Details: The structures are based on a total of 694 NOE restranints and 166 dihedral angle restraints. | ||||||||||||||||
NMR representative | Selection criteria: all calculated structures submited have the least restraint violation and the lowst energy. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |