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Yorodumi- PDB-7wgw: NMR Solution Structure of a cGMP Fill-in Vacancy G-quadruplex For... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wgw | ||||||
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Title | NMR Solution Structure of a cGMP Fill-in Vacancy G-quadruplex Formed in the Oxidized BLM Gene Promoter | ||||||
Components | DNA (20-MER) | ||||||
Keywords | DNA / 8-oxo-7 / 8-dihydroguanine / G-quadruplex / Bloom syndrome protein / guanine metabolite | ||||||
Function / homology | CYCLIC GUANOSINE MONOPHOSPHATE / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Wang, K.B. / Liu, Y. / Li, Y. / Li, J. / Dickerhoff, J. / Yang, M.H. / Yang, D. / Kong, L.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Oxidative Damage Induces a Vacancy G-Quadruplex That Binds Guanine Metabolites: Solution Structure of a cGMP Fill-in Vacancy G-Quadruplex in the Oxidized BLM Gene Promoter. Authors: Wang, K.B. / Liu, Y. / Li, Y. / Dickerhoff, J. / Li, J. / Yang, M.H. / Yang, D. / Kong, L.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wgw.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wgw.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wgw_validation.pdf.gz | 404.3 KB | Display | wwPDB validaton report |
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Full document | 7wgw_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 7wgw_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 7wgw_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wgw ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wgw | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 6314.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-PCG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 1.2 mM None BLM_G18O, 90% H2O/10% D2O / Label: none / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||||||||||||
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Sample | Conc.: 1.2 mM / Component: BLM_G18O / Isotopic labeling: None | ||||||||||||||||||||||||||||||||||||||||||
Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: QCI cryoprobe |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | |||||||||||||||
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: 10 |