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- PDB-8fb4: Structure of an alternating AT 16-mer bound by diamidine DB1476: ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fb4 | ||||||||||||||||||||||||||||
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Title | Structure of an alternating AT 16-mer bound by diamidine DB1476: 5'-GCTGGATATATCCAGC-3 | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / AT sequence / Minor groove | Function / homology | Chem-WFB / DNA / DNA (> 10) | ![]() Biological species | DNA molecule (others) | Method | ![]() ![]() ![]() ![]() Terrell, J.R. / Ogbonna, E.N. / Wilson, W.D. | Funding support | | ![]()
![]() ![]() Title: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences. Authors: Ogbonna, E.N. / Paul, A. / Farahat, A.A. / Terrell, J.R. / Mineva, E. / Ogbonna, V. / Boykin, D.W. / Wilson, W.D. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.2 KB | Display | ![]() |
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PDB format | ![]() | 63.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.4 MB | Display | ![]() |
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Full document | ![]() | 7.4 MB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ec1C ![]() 8ed6C ![]() 8edaC ![]() 8edbC ![]() 8f1sC ![]() 8f1vC ![]() 8f20C ![]() 8f2wC ![]() 8f2yC ![]() 8f94C ![]() 8fdpC ![]() 8fdqC ![]() 8fdrC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: DNA chain | Mass: 4898.191 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) #2: Chemical | #3: Chemical | ChemComp-CA / #4: 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: 2.36 Å3/Da / Density % sol: 47.95 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 1 mM DNA duplex with 3 mM DB1976 annealed in 7.5 mM HEPES, pH=6.6 mixed at a 1:1 ratio with well solution containing 10 mM HEPES, pH=8.6, 600 mM CaCl2, 38% PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022 |
Radiation | Monochromator: Horizontal double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→28.41 Å / Num. obs: 23742 / % possible obs: 99.21 % / Redundancy: 2 % / Biso Wilson estimate: 20.63 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01058 / Rpim(I) all: 0.01058 / Rrim(I) all: 0.01497 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.49→1.544 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1428 / Mean I/σ(I) obs: 5.06 / Num. unique obs: 2299 / CC1/2: 0.966 / CC star: 0.991 / Rpim(I) all: 0.1428 / Rrim(I) all: 0.202 / % possible all: 99.01 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 28.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→28.41 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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