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Open data
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Basic information
Entry | Database: PDB / ID: 7u38 | |||||||||
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Title | Pixantrone tethered DNA duplex | |||||||||
![]() | Pixantrone AP conjugate-modified DNA | |||||||||
![]() | DNA / Pixantrone / DNA structure / Pixantrone-AP / pixantrone conjugate / abasic site | |||||||||
Function / homology | DNA / DNA (> 10)![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pallan, P.S. / Egli, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Characterization of a Covalent Conjugate between Pixantrone and an Abasic Site in DNA Authors: Kellum Jr., A.H. / Pallan, P.S. / Terrell, J.T. / Fu, Y. / Noh, B. / Rizzo, C.J. / Egli, M. / Stone, M.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27.1 KB | Display | ![]() |
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PDB format | ![]() | 17 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 401.1 KB | Display | ![]() |
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Full document | ![]() | 401.1 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 4.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 3918.543 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: LVR is Pixantrone AP conjugate, CBR is 5-Bromo cytidine Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystallized from drops containing 2.2 M ammonium sulfate, and 2.8% to 3.8% PEG-400, in 0.1 M HEPES sodium |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→50 Å / Num. obs: 7367 / % possible obs: 99.9 % / Redundancy: 37.5 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.022 / Rrim(I) all: 0.133 / Χ2: 0.816 / Net I/σ(I): 3.9 / Num. measured all: 276573 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: 156.38 Å2 / Biso mean: 49.563 Å2 / Biso min: 5.56 Å2
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Refinement step | Cycle: final / Resolution: 2.49→27.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.492→2.557 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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