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- PDB-8ed6: 5'-CGCGAATTCGCG-3' and benzimidazole diamidine (DB1476) complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ed6 | ||||||||||||||||||||||||||||
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Title | 5'-CGCGAATTCGCG-3' and benzimidazole diamidine (DB1476) complex with ligand orientation II | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / SMALL MOLECULE / MINOR GROOVE | Function / homology | Chem-WFB / DNA / DNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() 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 | ![]() | 52 KB | Display | ![]() |
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PDB format | ![]() | 36.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 587.7 KB | Display | ![]() |
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Full document | ![]() | 587.7 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ec1C ![]() 8edaC ![]() 8edbC ![]() 8f1sC ![]() 8f1vC ![]() 8f20C ![]() 8f2wC ![]() 8f2yC ![]() 8f94C ![]() 8fb4C ![]() 8fdpC ![]() 8fdqC ![]() 8fdrC ![]() 1bnaS S: Starting model for refinement 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Label seq-ID: 1 - 12
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Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Self-complementary DNA (5'-CGCGAATTCGCG-3' bound by ligand (DB1476) in orientation II. Source: (synth.) ![]() #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-WFB / | #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: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRAHYDRATE, MAGNESIUM CHLORIDE HEXAHYDRATE, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2022 |
Radiation | Monochromator: double crystal - water cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→34.2 Å / Num. obs: 8886 / % possible obs: 99.5 % / Redundancy: 1.2 % / CC1/2: 1 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.63→1.69 Å / Num. unique obs: 807 / CC1/2: 1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BNA Resolution: 1.63→34.19 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 25.12 / Stereochemistry target values: ML
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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: 67.06 Å2 / Biso mean: 28.2968 Å2 / Biso min: 15.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.63→34.19 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 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 14.8156 Å / Origin y: 20.7737 Å / Origin z: 9.0632 Å
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Refinement TLS group |
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