+Open data
-Basic information
Entry | Database: PDB / ID: 8fdr | ||||||
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Title | Structure of a dodecamer complex: 5'-CGCGAAAAGCCG-3-DB1476 | ||||||
Components |
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Keywords | DNA / AT sequence / 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: 1.55 Å | ||||||
Authors | Ogbonna, E. / Wilson, W.D. | ||||||
Funding support | United States, 1items
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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. #1: Journal: To be published Title: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences Authors: Ogbonna, E.N. / Paul, A. / Faharat, A. / Terrell, J.R. / 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 | 8fdr.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fdr.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 8fdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fdr_validation.pdf.gz | 592.5 KB | Display | wwPDB validaton report |
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Full document | 8fdr_full_validation.pdf.gz | 592.5 KB | Display | |
Data in XML | 8fdr_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 8fdr_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/8fdr ftp://data.pdbj.org/pub/pdb/validation_reports/fd/8fdr | HTTPS FTP |
-Related structure data
Related structure data | 8ec1C 8ed6C 8edaC 8edbC 8f1sC 8f1vC 8f20C 8f2wC 8f2yC 8f94C 8fb4C 8fdpC 8fdqC 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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-Components
#1: DNA chain | Mass: 3681.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: DNA chain | Mass: 3645.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Chemical | ChemComp-WFB / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 47.16 % |
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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 HEXAHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25.52 Å / Num. obs: 104344 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 1 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.55→1.605 Å / Num. unique obs: 1011 / CC1/2: 0.992 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→25.52 Å / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.3651 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: 29.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→25.52 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.0772186674 Å / Origin y: 20.7722415333 Å / Origin z: 8.82441717769 Å
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Refinement TLS group | Selection details: all |