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Yorodumi- PDB-8f1v: A benzimidazole (DB1476) sequence-specific recognition of 5'-CGCA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f1v | ||||||
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Title | A benzimidazole (DB1476) sequence-specific recognition of 5'-CGCAAAAAAGCG-3' in B-orientation | ||||||
Components |
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Keywords | DNA / Minor groove binder / Minor groove / sequence recognition | ||||||
Function / homology | Chem-WFB / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ogbonna, E.N. / 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: J Org Chem / Year: 2014 Title: Design and synthesis of heterocyclic cations for specific DNA recognition: from AT-rich to mixed-base-pair DNA sequences. Authors: Chai, Y. / Paul, A. / Rettig, M. / Wilson, W.D. / Boykin, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f1v.cif.gz | 28.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f1v.ent.gz | 17.2 KB | Display | PDB format |
PDBx/mmJSON format | 8f1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f1v_validation.pdf.gz | 585.9 KB | Display | wwPDB validaton report |
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Full document | 8f1v_full_validation.pdf.gz | 586 KB | Display | |
Data in XML | 8f1v_validation.xml.gz | 3 KB | Display | |
Data in CIF | 8f1v_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/8f1v ftp://data.pdbj.org/pub/pdb/validation_reports/f1/8f1v | HTTPS FTP |
-Related structure data
Related structure data | 8ec1C 8ed6C 8edaC 8edbC 8f1sC 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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-Components
#1: DNA chain | Mass: 3689.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: DNA chain | Mass: 3635.362 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: 2.27 Å3/Da / Density % sol: 45.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, SODIUM CACOCYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM CHLORIDE, POTASSIUM 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: Jul 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25.33 Å / Num. obs: 4201 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 9.71 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 403 / CC1/2: 0.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BNA Resolution: 2.1→25.33 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 43.18 / 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: 65.97 Å2 / Biso mean: 47.1386 Å2 / Biso min: 39.02 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→25.33 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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