+Open data
-Basic information
Entry | Database: PDB / ID: 8bna | ||||||||||||||||||
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Title | BINDING OF HOECHST 33258 TO THE MINOR GROOVE OF B-DNA | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | Chem-HT / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Pjura, P.E. / Grzeskowiak, K. / Dickerson, R.E. | Citation | Journal: J.Mol.Biol. / Year: 1987 Title: Binding of Hoechst 33258 to the minor groove of B-DNA. Authors: Pjura, P.E. / Grzeskowiak, K. / Dickerson, R.E. #1: Journal: J.Med.Chem. / Year: 1986 Title: Isohelical Analysis of DNA Groove-Binding Drugs Authors: Goodsell, D. / Dickerson, R.E. #2: Journal: J.Mol.Biol. / Year: 1985 Title: Binding of an Antitumor Drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G Authors: Kopka, M.L. / Yoon, C. / Goodsell, D.S. / Pjura, P. / Dickerson, R.E. #3: Journal: To be Published Title: Drugs and Minor Groove Binding in B-DNA Netropsin and Hoechst 33258 Authors: Kopka, M.L. / Pjura, P.E. / Goodsell, D.S. / Dickerson, R.E. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985 Title: The Molecular Origin of DNA-Drug Specificity in Netropsin and Distamycin Authors: Kopka, M.L. / Yoon, C. / Goodsell, D.S. / Pjura, P. / Dickerson, R.E. #5: Journal: Nature / Year: 1980 Title: Crystal Structure Analysis of a Complete Turn of B-DNA Authors: Wing, R. / Drew, H.R. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bna.cif.gz | 29.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bna.ent.gz | 19.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bna_validation.pdf.gz | 679.3 KB | Display | wwPDB validaton report |
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Full document | 8bna_full_validation.pdf.gz | 689.1 KB | Display | |
Data in XML | 8bna_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 8bna_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/8bna ftp://data.pdbj.org/pub/pdb/validation_reports/bn/8bna | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 #2: Chemical | ChemComp-HT / | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Type: SYNTEX P1 / Detector: DIFFRACTOMETER |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. obs: 3487 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 2.2 Å / Observed criterion σ(I): 0.28 |
-Processing
Software | Name: JACK-LEVITT / Classification: refinement | ||||||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(F): 0 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor all: 0.191 / Rfactor obs: 0.14 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |