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Yorodumi- PDB-8ec1: 5'-CGCGAATTCGCG-3' and benzimidazole diamidine (DB1476) comlpex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ec1 | ||||||||||||||||||||||||||||
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Title | 5'-CGCGAATTCGCG-3' and benzimidazole diamidine (DB1476) comlpex with ligand orientation I | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / MINOR GROOVE / SMALL MOLECULE | Function / homology | Chem-WFB / DNA / DNA (> 10) | Function and homology information Biological species | Homo (humans) | 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 | 8ec1.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ec1.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ec1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ec1_validation.pdf.gz | 589.3 KB | Display | wwPDB validaton report |
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Full document | 8ec1_full_validation.pdf.gz | 589.3 KB | Display | |
Data in XML | 8ec1_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 8ec1_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/8ec1 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/8ec1 | HTTPS FTP |
-Related structure data
Related structure data | 8ed6C 8edaC 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'-CGCGAATTCGCG-3') bound by ligand (DB1476) in a type I orientation. Source: (synth.) Homo (humans) #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: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: magnesium chloride hexahydrate, sodium chloride, potassium chloride, double-stranded DNA, MPD ,spermine tetrahydrate, sodium cacodylate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.98 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2022 Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror water |
Radiation | Monochromator: double crystal - water cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→34.2 Å / Num. obs: 8886 / % possible obs: 99 % / Redundancy: 1.2 % / CC1/2: 1 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.63→1.69 Å / Num. unique obs: 807 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BNA Resolution: 1.63→34.19 Å / SU B: 25.89 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 0.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.89 Å2 / Biso mean: 28 Å2 / Biso min: 16.63 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
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Refinement TLS params. | Method: refined / Origin x: 14.7949 Å / Origin y: 20.9234 Å / Origin z: 9.0799 Å
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Refinement TLS group |
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