+Open data
-Basic information
Entry | Database: PDB / ID: 1ql5 | ||||||
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Title | DNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT | ||||||
Components |
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Keywords | DNA / DEOXYRIBONUCLEIC ACID / DNA PHOTOPRODUCT / (6-4) ADDUCT / MUTAGENESIS | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, FULL RELAXATION MATRIX REFINEMENT | ||||||
Model type details | MINIMIZED AVERAGE | ||||||
Authors | Lee, J.-H. / Hwang, G.-S. / Choi, B.-S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2000 Title: Solution Structure of a DNA Decamer Duplex Containing the 3' T.T Base Pair of the Cis-Syn Cyclobutane Pyrimidine Dimer: Implication for the Mutagenic Property of the Cis-Syn Dimer. Authors: Lee, J.-H. / Choi, Y.-J. / Choi, B.-S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ql5.cif.gz | 23.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ql5.ent.gz | 15.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ql5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ql5_validation.pdf.gz | 342.3 KB | Display | wwPDB validaton report |
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Full document | 1ql5_full_validation.pdf.gz | 348.7 KB | Display | |
Data in XML | 1ql5_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 1ql5_validation.cif.gz | 3.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1ql5 ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1ql5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3009.013 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: CYCLOBUTANE RING FORMED BETWEEN C5-C6(T5) AND C5-C6(T6) DOUBLE BONDS |
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#2: DNA chain | Mass: 3076.015 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: NOESY |
NMR details | Text: MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING SA METHOD WITH DISTANCE RESTRAINTS AND FULL RELAXATION MATRIX REFINEMENT WITH NOE INTENSITY RESTRAINTS OF 50, 80, 160 MS MIXING TIMES |
-Sample preparation
Sample conditions | pH: 6.6 / Temperature: 274.0 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, FULL RELAXATION MATRIX REFINEMENT Software ordinal: 1 Details: MISMATCHED BASE PAIRING OF 3'-T OF CIS-SYN DIMER WITH A RESIDUE. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 8 / Conformers submitted total number: 1 |