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- PDB-129d: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') COMPLEXED WITH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 129d | ||||||||||||||||||
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Title | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') COMPLEXED WITH HOECHST 33342 | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | Chem-HT1 / DNA / DNA (> 10) | ![]() Method | ![]() ![]() Sriram, M. / Van Der Marel, G.A. / Roelen, H.L.P.F. / Van Boom, J.H. / Wang, A.H.-J. | ![]() ![]() Title: Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342. Authors: Sriram, M. / van der Marel, G.A. / Roelen, H.L. / van Boom, J.H. / Wang, A.H. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.1 KB | Display | ![]() |
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PDB format | ![]() | 16.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 391.6 KB | Display | ![]() |
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Full document | ![]() | 410.4 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 6 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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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-HT1 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. obs: 1735 / Observed criterion σ(F): 2 |
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Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2.25 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 2.25 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.25 Å / Num. reflection obs: 1735 / σ(F): 2 / Rfactor obs: 0.168 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d / Dev ideal: 0.02 |