+Open data
-Basic information
Entry | Database: PDB / ID: 8eda | ||||||||||||||||||||||||||||
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Title | An alternating AT dodecamer benzimidazole (DB1476) complex | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / SMALL MOLECULE / MINOR GROOVE | Function / homology | Chem-WFB / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | Authors | Ogbonna, E.N. / Wilson, W.D. | Funding support | United States, 1items |
Citation | Journal: Acs Bio Med Chem Au / Year: 2023 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eda.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eda.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 8eda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eda_validation.pdf.gz | 602.9 KB | Display | wwPDB validaton report |
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Full document | 8eda_full_validation.pdf.gz | 603.9 KB | Display | |
Data in XML | 8eda_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 8eda_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/8eda ftp://data.pdbj.org/pub/pdb/validation_reports/ed/8eda | HTTPS FTP |
-Related structure data
Related structure data | 8ec1C 8ed6C 8edbC 8f1sC 8f1vC 8f20C 8f2wC 8f2yC 8f94C 8fb4C 8fdpC 8fdqC 8fdrC 1bnaS S: Starting model for refinement 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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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: A self-complementary DNA (5'-CGCGATATCGCG-3') bound by the ligand (DB1476). Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-WFB / | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM CHLORIDE, MAGNESIUM CHLORIDE HEXAHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 18, 2022 |
Radiation | Monochromator: double-crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→34.21 Å / Num. obs: 8949 / % possible obs: 99.2 % / Redundancy: 1.2 % / CC1/2: 1 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.63→1.69 Å / Num. unique obs: 840 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BNA Resolution: 1.63→34.21 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.12 / 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: 69.09 Å2 / Biso mean: 26.9094 Å2 / Biso min: 14.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.63→34.21 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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