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Yorodumi- PDB-7ku4: DNA-DB818 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ku4 | ||||||||||||||||||||||||||||
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Title | DNA-DB818 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents a binding site for the heterocyclic small molecule (DB818). | ||||||||||||||||||||||||||||
Components | 1:(5'-D(*Keywords | DNA / DNA-molecule complex | Function / homology | Chem-D1B / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | Authors | Ogbonna, E. / Fang, Z. / Wilson, W.D. | Funding support | United States, 1items |
Citation | Journal: Bioorg.Med.Chem. / Year: 2022 | Title: Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines. Authors: Ogbonna, E.N. / Paul, A. / Ross Terrell, J. / Fang, Z. / Chen, C. / Poon, G.M.K. / 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 | 7ku4.cif.gz | 28.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ku4.ent.gz | 16.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ku4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ku4_validation.pdf.gz | 608.4 KB | Display | wwPDB validaton report |
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Full document | 7ku4_full_validation.pdf.gz | 609.8 KB | Display | |
Data in XML | 7ku4_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 7ku4_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/7ku4 ftp://data.pdbj.org/pub/pdb/validation_reports/ku/7ku4 | HTTPS FTP |
-Related structure data
Related structure data | 7kwkC 1bnaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-D1B / | #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 meas: 0.717 Mg/m3 / Density % sol: 46.79 % / Description: Rod shaped crystal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% MPD, 0.040M Sodium Cacodylate trihydrate, 0.012 Spermine Tetrahydrate, 0.080M Sodium Chloride, 0.020M Magnesium chloride hexahydrate Temp details: Temperature was kept constant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.14 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 28, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SINGLE CRYSTAL Si (200) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.14 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 9102 / % possible obs: 96.6 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.021 / Rrim(I) all: 0.073 / Χ2: 0.981 / Net I/σ(I): 12.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BNA Resolution: 1.6→34.21 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.75 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 33.98 Å2 / Biso mean: 12.119 Å2 / Biso min: 4.92 Å2
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Refinement step | Cycle: final / Resolution: 1.6→34.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.636 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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