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Yorodumi- PDB-6sx6: Guanine-rich oligonucleotide with 5'-GC end form G-quadruplex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sx6 | ||||||
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Title | Guanine-rich oligonucleotide with 5'-GC end form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pairs | ||||||
Components | GCn | ||||||
Keywords | DNA / G-quadruplex / A(GGGG)A hexad / GCGC-quartet / 5'-GC ends | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Pavc, D. / Wang, B. / Spindler, L. / Drevensek-Olenik, I. / Plavec, J. / Sket, P. | ||||||
Funding support | Slovenia, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly. Authors: Pavc, D. / Wang, B. / Spindler, L. / Drevensek-Olenik, I. / Plavec, J. / Sket, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sx6.cif.gz | 156 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sx6.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 6sx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sx6_validation.pdf.gz | 344 KB | Display | wwPDB validaton report |
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Full document | 6sx6_full_validation.pdf.gz | 404.8 KB | Display | |
Data in XML | 6sx6_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 6sx6_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/6sx6 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/6sx6 | HTTPS FTP |
-Related structure data
Related structure data | 6sykC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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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: 3833.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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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: 6 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 10 |