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Yorodumi- PDB-1d54: ANTHRACYCLINE BINDING TO DNA: HIGH RESOLUTION STRUCTURE OF D(TGTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d54 | ||||||||||||||||||
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Title | ANTHRACYCLINE BINDING TO DNA: HIGH RESOLUTION STRUCTURE OF D(TGTACA) COMPLEXED WITH 4'-EPIADRIAMYCIN | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | 4'-EPIDOXORUBICIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | Authors | Leonard, G.A. / Brown, T. / Hunter, W.N. | Citation | Journal: Eur.J.Biochem. / Year: 1992 | Title: Anthracycline binding to DNA. High-resolution structure of d(TGTACA) complexed with 4'-epiadriamycin. Authors: Leonard, G.A. / Brown, T. / Hunter, W.N. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d54.cif.gz | 14.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d54.ent.gz | 8 KB | Display | PDB format |
PDBx/mmJSON format | 1d54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d54_validation.pdf.gz | 714.9 KB | Display | wwPDB validaton report |
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Full document | 1d54_full_validation.pdf.gz | 717.1 KB | Display | |
Data in XML | 1d54_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 1d54_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d54 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d54 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1808.229 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-DM6 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.18 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU AFC-5 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. all: 11022 / Num. obs: 5644 |
Reflection | *PLUS Highest resolution: 1.3 Å / Num. measured all: 11022 / Rmerge(I) obs: 0.064 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.4→7 Å / σ(F): 3 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.4→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 7 Å / σ(F): 3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |