[English] 日本語
Yorodumi- PDB-2l2u: NMR Solution Structures of +3 (5' staggered) Bistranded Abasic Si... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l2u | ||||||
---|---|---|---|---|---|---|---|
Title | NMR Solution Structures of +3 (5' staggered) Bistranded Abasic Site Lesions in DNA | ||||||
Components |
| ||||||
Keywords | DNA / Abasic Lesion / Bistranded DNA Lesions / Clustered DNA damage / Multiple DNA Damage / Ionizing Radiation | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / molecular dynamics, DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Hazel, R.D. / de los Santos, C. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: NMR solution structures of clustered abasic site lesions in DNA: structural differences between 3'-staggered (-3) and 5'-staggered (+3) bistranded lesions. Authors: Hazel, R.D. / de los Santos, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2l2u.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2l2u.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 2l2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2l2u_validation.pdf.gz | 322.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2l2u_full_validation.pdf.gz | 356.9 KB | Display | |
Data in XML | 2l2u_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 2l2u_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/2l2u ftp://data.pdbj.org/pub/pdb/validation_reports/l2/2l2u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 4180.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide |
---|---|
#2: DNA chain | Mass: 4131.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: unknown mM DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3'), unknown mM DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3'), 100% D2O Solvent system: 100% D2O | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample |
| |||||||||
Sample conditions | pH: 6.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
---|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: molecular dynamics, DGSA-distance geometry simulated annealing Software ordinal: 1 Details: Authors indicate chirality error at DT8 in model 1 due to flexibility of the DNA duplex in solution | ||||||||||||
NMR constraints | NOE constraints total: 554 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 20 / Conformers submitted total number: 4 |