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Yorodumi- PDB-7qvq: Human telomeric DNA G-quadruplex of a gold(III) complex containin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qvq | ||||||||||||
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Title | Human telomeric DNA G-quadruplex of a gold(III) complex containing the 2,4,6-tris (2-pyrimidyl)-1,3,5-triazine ligand | ||||||||||||
Components | human telomeric DNA | ||||||||||||
Keywords | DNA / DRUG-DNA COMPLEX / telomeric G-quadruplex | ||||||||||||
Function / homology | Chem-I6K / : / DNA / DNA (> 10) Function and homology information | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Bazzicalupi, C. / Ryde, U. / Gratteri, P. / Bergmann, J. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis. Authors: Bazzicalupi, C. / Bonardi, A. / Biver, T. / Ferraroni, M. / Papi, F. / Savastano, M. / Lombardi, P. / Gratteri, P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qvq.cif.gz | 28.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qvq.ent.gz | 18.7 KB | Display | PDB format |
PDBx/mmJSON format | 7qvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qvq_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7qvq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7qvq_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 7qvq_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/7qvq ftp://data.pdbj.org/pub/pdb/validation_reports/qv/7qvq | HTTPS FTP |
-Related structure data
Related structure data | 7zurC 8aadC 6h5rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 7591.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-I6K / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: isopropanol, potassium cacodylate, Li2SO4, MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→35.76 Å / Num. obs: 2753 / % possible obs: 98.4 % / Redundancy: 6.3 % / CC1/2: 0.957 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.222 / Net I/σ(I): 5.68 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.103 / Num. unique obs: 404 / CC1/2: 0.712 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H5R Resolution: 2.4→35.76 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.982 / SU ML: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 315.83 Å2 / Biso mean: 57.072 Å2 / Biso min: 23.98 Å2
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Refinement step | Cycle: final / Resolution: 2.4→35.76 Å
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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