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Yorodumi- PDB-1d58: THE MOLECULAR STRUCTURE OF A 4'-EPIADRIAMYCIN COMPLEX WITH D(TGAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d58 | ||||||||||||||||||
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Title | THE MOLECULAR STRUCTURE OF A 4'-EPIADRIAMYCIN COMPLEX WITH D(TGATCA) AT 1.7 ANGSTROM RESOLUTION-COMPARISON WITH THE STRUCTURE OF 4'-EPIADRIAMYCIN D(TGTACA) AND D(CGATCG) COMPLEXES | ||||||||||||||||||
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: 1.7 Å | Authors | Langlois D'Estaintot, B. / Gallois, B. / Brown, T. / Hunter, W.N. | Citation | Journal: Nucleic Acids Res. / Year: 1992 | Title: The molecular structure of a 4'-epiadriamycin complex with d(TGATCA) at 1.7A resolution: comparison with the structure of 4'-epiadriamycin d(TGTACA) and d(CGATCG) complexes. Authors: Langlois d'Estaintot, B. / Gallois, B. / 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 | 1d58.cif.gz | 14.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d58.ent.gz | 7.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d58_validation.pdf.gz | 737.4 KB | Display | wwPDB validaton report |
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Full document | 1d58_full_validation.pdf.gz | 743.3 KB | Display | |
Data in XML | 1d58_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1d58_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d58 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d58 | 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 ℃ / Method: vapor diffusion, sitting drop / pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU AFC-5 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.7 Å / Num. all: 10067 / Num. obs: 5730 |
Reflection | *PLUS Highest resolution: 1.7 Å / Rmerge(I) obs: 0.102 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||
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Refinement | Resolution: 1.7→7 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.7→7 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 7 Å / σ(F): 2 / Rfactor obs: 0.202 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |