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Yorodumi- PDB-1tqr: NMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tqr | ||||||
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Title | NMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to the extremity of the U5 LTR of the HIV-1 genome | ||||||
Components | (DNA HIV-1 U5 LTR extremity) x 2 | ||||||
Keywords | DNA / double helix | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / torsion angle dynamics including classical, RDC constraints | ||||||
Authors | Renisio, J.G. / Cosquer, S. / Cherrak, I. / El Antri, S. / Mauffret, O. / Fermandjian, S. | ||||||
Citation | Journal: NUCLEIC ACIDS RES. / Year: 2005 Title: Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase Authors: Renisio, J.G. / Cosquer, S. / Cherrak, I. / El Antri, S. / Mauffret, O. / Fermandjian, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tqr.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tqr.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/1tqr ftp://data.pdbj.org/pub/pdb/validation_reports/tq/1tqr | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 5235.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Classical phosphoramidite chemistry |
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#2: DNA chain | Mass: 5177.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Classical phosphoramidite chemistry |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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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 | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
-Processing
NMR software | Name: CNS / Version: 0.9a / Classification: refinement |
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Refinement | Method: torsion angle dynamics including classical, RDC constraints Software ordinal: 1 Details: in the first stage the classical constraints were used with TAD at high temperature, in a second stage the RDC were gradually added with TAD at low temperature (200K) |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 9 |