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Open data
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Basic information
Entry | Database: PDB / ID: 7d31 | ||||||||||||||||||||||||||||
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Title | The TBA-Pb2+ complex in P41212 space group | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Quadruplex / Pb2+-binding / DNA aptamer | Function / homology | LEAD (II) ION / DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Liu, H.H. / Gao, Y.Q. / Sheng, J. / Gan, J.H. | Funding support | | ![]()
![]() ![]() Title: Structure-guided development of Pb 2+ -binding DNA aptamers. Authors: Liu, H. / Gao, Y. / Mathivanan, J. / Shen, F. / Chen, X. / Li, Y. / Shao, Z. / Zhang, Y. / Shao, Q. / Sheng, J. / Gan, J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.7 KB | Display | ![]() |
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PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 918.6 KB | Display | ![]() |
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Full document | ![]() | 918.5 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DG / End label comp-ID: DG / Auth seq-ID: 1 - 15 / Label seq-ID: 1 - 15
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Components
#1: DNA chain | Mass: 4743.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #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 | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % / Description: Block |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% v/v MPD, 40 mM sodium cacodylate pH 7.0, 12 mM spermine tetra-HCl, and 80 mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.396→30 Å / Num. obs: 16599 / % possible obs: 97.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.028 / Rrim(I) all: 0.113 / Χ2: 2.689 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 33.15 Å2 / Biso mean: 18.9052 Å2 / Biso min: 11.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.396→27.225 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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