+Open data
-Basic information
Entry | Database: PDB / ID: 5gwq | ||||||||||||||||||||||||||||
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Title | Structure of two TTTA repeats | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Minidumbbell / type II loop | Function / homology | DNA | Function and homology information Biological species | Staphylococcus aureus (bacteria) | Method | SOLUTION NMR / restrained molecular dynamics | Authors | Guo, P. / Lam, S.L. | Funding support | Hong Kong, 1items |
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 | Title: Minidumbbell: A New Form of Native DNA Structure Authors: Guo, P. / Lam, S.L. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gwq.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gwq.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 5gwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gwq_validation.pdf.gz | 315.4 KB | Display | wwPDB validaton report |
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Full document | 5gwq_full_validation.pdf.gz | 403.1 KB | Display | |
Data in XML | 5gwq_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 5gwq_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/5gwq ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gwq | 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: 2406.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) |
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#2: Chemical | ChemComp-NA / |
-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 DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3'), 10 mM sodium phosphate, 0.1 mM DSS, 100% D2O Label: 1H / Solvent system: 100% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.02 M / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 278 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: restrained molecular dynamics / Software ordinal: 2 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 1000 / Conformers submitted total number: 20 |