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Yorodumi- PDB-2l2v: NMR Solution Structures of -3 (3' staggered) Bistranded Abasic Si... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l2v | ||||||
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Title | NMR Solution Structures of -3 (3' staggered) Bistranded Abasic Site Lesions in DNA | ||||||
Components |
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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 / distance geometry, molecular dynamics | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l2v.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l2v.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 2l2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2l2v_validation.pdf.gz | 322.1 KB | Display | wwPDB validaton report |
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Full document | 2l2v_full_validation.pdf.gz | 364.6 KB | Display | |
Data in XML | 2l2v_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 2l2v_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/2l2v ftp://data.pdbj.org/pub/pdb/validation_reports/l2/2l2v | HTTPS FTP |
-Related 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: 4180.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide |
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#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 | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: unknown mM DNA (5'-D(*CP*AP*GP*CP*TP*AP*TP*GP*(3DR)P*GP*AP*AP*GP*C)-3'), unknown mM DNA (5'-D(*GP*CP*TP*TP*CP*AP*CP*AP*(3DR)P*AP*GP*CP*TP*G)-3'), 100% D2O Solvent system: 100% D2O | |||||||||
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Sample |
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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 |
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-Processing
NMR software |
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Refinement | Method: distance geometry, molecular dynamics / Software ordinal: 1 | ||||||||||||
NMR constraints | NOE constraints total: 533 | ||||||||||||
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 |