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Yorodumi- PDB-5j3g: Solution NMR structure of PT-free dsDNA from Streptomyces lividans -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j3g | ||||||
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Title | Solution NMR structure of PT-free dsDNA from Streptomyces lividans | ||||||
Components |
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Keywords | DNA / dsDNA PT-free NMR Streptomyces lividans | ||||||
Function / homology | DNA Function and homology information | ||||||
Biological species | Streptomyces lividans (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Lan, W. / Cao, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: Structural investigation into physiological DNA phosphorothioate modification Authors: Lan, W. / Hu, Z. / Shen, J. / Wang, C. / Jiang, F. / Liu, H. / Long, D. / Liu, M. / Cao, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j3g.cif.gz | 227.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j3g.ent.gz | 189.9 KB | Display | PDB format |
PDBx/mmJSON format | 5j3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j3g_validation.pdf.gz | 393.3 KB | Display | wwPDB validaton report |
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Full document | 5j3g_full_validation.pdf.gz | 563.8 KB | Display | |
Data in XML | 5j3g_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 5j3g_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/5j3g ftp://data.pdbj.org/pub/pdb/validation_reports/j3/5j3g | 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: 3030.981 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans (bacteria) / Production host: Streptomyces lividans (bacteria) |
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#2: DNA chain | Mass: 3061.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans (bacteria) / Production host: Streptomyces lividans (bacteria) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1.0 mM PT-free dsDNA, 100 mM NaCl, 40 mM NaPO4, 90% H2O/10% D2O Label: PT-free dsDNA / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 360 mM / Ionic strength err: 0.1 / pH: 7.0 / Temperature err: 0.1
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |