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Yorodumi- PDB-1qda: Crystal structure of epidoxorubicin-formaldehyde virtual crosslin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qda | ||||||||||||||||||
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Title | Crystal structure of epidoxorubicin-formaldehyde virtual crosslink of DNA | ||||||||||||||||||
Components | 5' -D(CP*Keywords | DNA / DOUBLE HELIX / DRUG-DNA COMPLEX | Function / homology | 4'-EPIDOXORUBICIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | Authors | Podell, E.R. / Harrington, D.J. / Taatjes, D.J. / Koch, T.H. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystal structure of epidoxorubicin-formaldehyde virtual crosslink of DNA and evidence for its formation in human breast-cancer cells. Authors: Podell, E.R. / Harrington, D.J. / Taatjes, D.J. / Koch, T.H. #1: Journal: Curr.Pharm.Des. / Year: 1998 Title: A redox pathway leading to the alkylation of nucleic acids by doxorubicin and related anthracyclines: application to the design of antitumor drugs for resistant cancer. Authors: Taatjes, D.J. / Fenick, D.J. / Gaudiano, G. / Koch, T.H. #2: Journal: J.Med.Chem. / Year: 1998 Title: Epidoxoform: A Hydrolytically More Stable Anthracycline-Formaldehyde Conjugate Toxic to Resistant Tumor Cells Authors: Taatjes, D.J. / Fenick, D.J. / Koch, T.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qda.cif.gz | 15.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qda.ent.gz | 9.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qda_validation.pdf.gz | 743.5 KB | Display | wwPDB validaton report |
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Full document | 1qda_full_validation.pdf.gz | 744.9 KB | Display | |
Data in XML | 1qda_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 1qda_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/1qda ftp://data.pdbj.org/pub/pdb/validation_reports/qd/1qda | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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 Details: DOXORUBICIN COVALENTLY ATTACHED TO N2(G4) VIA METHYLENE BRIDGE |
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#2: Chemical | ChemComp-DM6 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.82 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, FORMALDEHYDE, CACODYLATE, SPERMINE, BARIUM CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
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 RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 3101 / Num. obs: 3101 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.309 / % possible all: 82.7 |
Reflection | *PLUS Num. measured all: 47174 |
Reflection shell | *PLUS % possible obs: 82.7 % / Num. unique obs: 2482 |
-Processing
Software |
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Refinement | Resolution: 1.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN Details: USED ALL THE REFLECTIONS IN THE FINAL SERIES OF REFINEMENT CYCLES
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 17.3 % / Rfactor all: 0.2164 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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