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Yorodumi- PDB-6bna: BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bna | ||||||||||||||||||
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Title | BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | NETROPSIN / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.21 Å | Authors | Kopka, M.L. / Yoon, C. / Goodsell, D. / Pjura, P. / Dickerson, R.E. | Citation | 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. / Pjura, P. / Dickerson, R.E. #1: Journal: Structure and Motion. Membranes, Nucleic Acids and Protein. Title: The Binding of Netropsin to Double-Helical B-DNA of Sequence C-G-C-G-A-A-T-T-BrC-G-C-G. Single Crystal X-Ray Structure Analysis Authors: Kopka, M.L. / Pjura, P. / Yoon, C. / Goodsell, D. / Dickerson, R.E. #2: 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. / Pjura, P. / 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 | 6bna.cif.gz | 27.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bna.ent.gz | 17.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bna_validation.pdf.gz | 600.9 KB | Display | wwPDB validaton report |
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Full document | 6bna_full_validation.pdf.gz | 618.6 KB | Display | |
Data in XML | 6bna_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 6bna_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/6bna ftp://data.pdbj.org/pub/pdb/validation_reports/bn/6bna | 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: 3742.288 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.76 % | |||||||||||||||||||||||||||||||||||
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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 Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Detector: DIFFRACTOMETER |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. obs: 3240 |
Reflection | *PLUS Highest resolution: 2.2 Å |
-Processing
Software | Name: JACK-LEVITT / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.21→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.21→8 Å
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Refinement | *PLUS Highest resolution: 2.21 Å / Lowest resolution: 8 Å / Num. reflection all: 3140 / σ(F): 2 / Rfactor all: 0.257 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |