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- PDB-474d: A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 474d | ||||||||||||||||||
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Title | A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2 | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA/RNA / DOUBLE HELIX / DOUBLE DRUG IN MINOR GROOVE / COMPLEXED WITH DRUG / MODIFIED / MISMATCHED | Function / homology | NETROPSIN / DNA | ![]() Method | ![]() ![]() Chen, X. / Rao, S.T. / Sekar, K. / Sundaralingam, M. | ![]() ![]() Title: A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2. Authors: Chen, X. / Mitra, S.N. / Rao, S.T. / Sekar, K. / Sundaralingam, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30.5 KB | Display | ![]() |
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PDB format | ![]() | 24.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 552.8 KB | Display | ![]() |
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Full document | ![]() | 561.4 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3050.807 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | ChemComp-NT / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. obs: 8747 / % possible obs: 73 % / Observed criterion σ(I): 1.4 / Redundancy: 2.04 % / Rmerge(I) obs: 0.045 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 15 Å / Num. obs: 4284 / % possible obs: 73 % / Observed criterion σ(I): 1.4 / Redundancy: 2.04 % / Rmerge(I) obs: 0.061 |
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Processing
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Refinement | Resolution: 2.4→8 Å / σ(F): 4
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8 Å / % reflection Rfree: 5 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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