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Yorodumi- PDB-1d33: Formaldehyde cross-links daunorubicin and DNA efficiently: HPLC a... -
+Open data
-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 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | DAUNOMYCIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | Authors | Wang, A.H.-J. / Gao, Y.-G. / Liaw, Y.-C. / Li, Y.-K. | Citation | Journal: Biochemistry / Year: 1991 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d33.cif.gz | 15.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d33.ent.gz | 9.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d33_validation.pdf.gz | 415.3 KB | Display | wwPDB validaton report |
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Full document | 1d33_full_validation.pdf.gz | 420.7 KB | Display | |
Data in XML | 1d33_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 1d33_validation.cif.gz | 3.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d33 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d33 | HTTPS FTP |
-Related structure data
-Links
-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: X-RAY DIFFRACTION |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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 |
-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 |