+Open data
-Basic information
Entry | Database: PDB / ID: 1agl | ||||||||||||||||||
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Title | STRUCTURE OF A DNA-BISDAUNOMYCIN COMPLEX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | 4-METHYLBENZYL-N-BIS[DAUNOMYCIN] / DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | Authors | Hu, G.G. / Shui, X. / Leng, F. / Priebe, W. / Chaires, J.B. / Williams, L.D. | Citation | Journal: Biochemistry / Year: 1997 | Title: Structure of a DNA-bisdaunomycin complex. Authors: Hu, G.G. / Shui, X. / Leng, F. / Priebe, W. / Chaires, J.B. / Williams, L.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1agl.cif.gz | 15 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1agl.ent.gz | 7.5 KB | Display | PDB format |
PDBx/mmJSON format | 1agl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1agl_validation.pdf.gz | 393.3 KB | Display | wwPDB validaton report |
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Full document | 1agl_full_validation.pdf.gz | 392.4 KB | Display | |
Data in XML | 1agl_validation.xml.gz | 1.7 KB | Display | |
Data in CIF | 1agl_validation.cif.gz | 2.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1agl ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1agl | 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: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-BDA / |
#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: 2.84 Å3/Da / Density % sol: 56.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: May 1, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→12 Å / Num. all: 11192 / Num. obs: 2058 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 6.76 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.5 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 12 Å / % possible obs: 93 % / Num. measured all: 11192 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DDF045 Resolution: 2.2→10 Å / σ(F): 3
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å
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Xplor file | Serial no: 1 / Param file: PARDNA.PRO / Topol file: TOPDNA.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 3 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 3.1 |