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- PDB-1d33: Formaldehyde cross-links daunorubicin and DNA efficiently: HPLC a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d33 | ||||||||||||||||||
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Title | Formaldehyde cross-links daunorubicin and DNA efficiently: HPLC and X-RAY diffraction studies | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | DAUNOMYCIN / DNA | ![]() Method | ![]() ![]() Wang, A.H.-J. / Gao, Y.-G. / Liaw, Y.-C. / Li, Y.-K. | ![]() ![]() Title: Formaldehyde cross-links daunorubicin and DNA efficiently: HPLC and X-ray diffraction studies. Authors: Wang, A.H. / Gao, Y.G. / Liaw, Y.C. / Li, Y.K. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.8 KB | Display | ![]() |
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PDB format | ![]() | 9.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.3 KB | Display | ![]() |
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Full document | ![]() | 420.7 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 3.4 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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Unit cell |
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Components
#1: DNA chain | Mass: 1824.232 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-DM1 / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | A METHYLENE GROUP LINKS THE N3* ATOM OF DAUNOMYCIN |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.99 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.5 Å / Observed criterion σ(F): 3 |
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Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 1.5 Å / σ(F): 3 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 1.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.5 Å / σ(F): 3 / Rfactor obs: 0.185 / Num. reflection obs: 2229 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |