+Open data
-Basic information
Entry | Database: PDB / ID: 8ask | ||||||
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Title | Crystal structure of d(GCCCACCACGGC) | ||||||
Components |
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Keywords | DNA / Ligand / Interaction | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | DNA molecule (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.955 Å | ||||||
Authors | Sbirkova-Dimitrova, H.I. / Shivachev, B.L. / Rusev, R. / Heroux, A. / Doukov, T. / Kuvandjiev, N. | ||||||
Funding support | Bulgaria, 1items
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Citation | Journal: Crystals / Year: 2022 Title: Structural Characterization of Alzheimer DNA Promoter Sequences from the Amyloid Precursor Gene in the Presence of Thioflavin T and Analogs Authors: Sbirkova-Dimitrova, H. / Rusew, R. / Kuvandjiev, N. / Heroux, A. / Doukov, T. / Shivachev, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ask.cif.gz | 24.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ask.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ask.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ask_validation.pdf.gz | 376.9 KB | Display | wwPDB validaton report |
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Full document | 8ask_full_validation.pdf.gz | 376.8 KB | Display | |
Data in XML | 8ask_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 8ask_validation.cif.gz | 2.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/8ask ftp://data.pdbj.org/pub/pdb/validation_reports/as/8ask | HTTPS FTP |
-Related structure data
Related structure data | 8ashC 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: 3593.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DNA molecule (others) / Production host: Synthesium (invertebrata) |
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#2: DNA chain | Mass: 3735.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DNA molecule (others) / Production host: Synthesium (invertebrata) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 20%MPD, 120mMMgCl2, 60mM NaCaCo, 2mM Spermine |
-Data collection
Diffraction | Mean temperature: 270 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 2 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→35.59 Å / Num. obs: 2783 / % possible obs: 96.95 % / Redundancy: 9.2 % / CC1/2: 0.992 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.97→3.02 Å / Num. unique obs: 1399 / CC1/2: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: X3DNA Resolution: 2.955→35.59 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.891 / SU B: 27.017 / SU ML: 0.398 / Cross valid method: NONE / ESU R Free: 0.413 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.593 Å2
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Refinement step | Cycle: LAST / Resolution: 2.955→35.59 Å
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Refine LS restraints |
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LS refinement shell |
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