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Yorodumi- PDB-1fdg: BINDING OF A MACROCYCLIC BISACRIDINE AND AMETANTRONE TO CGTACG IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fdg | ||||||||||||||||||||
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Title | BINDING OF A MACROCYCLIC BISACRIDINE AND AMETANTRONE TO CGTACG INVOLVES SIMILAR UNUSUAL INTERCALATION PLATFORMS (AMETANTRONE COMPLEX) | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / High resolution crystal structure / intercalation platform / MAD / anticancer drug / drug-DNA complex / metal ions / tertiary base pairs | Function / homology | Chem-9TA / : / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | Authors | Yang, X.-L. / Robinson, H. / Gao, Y.-G. / Wang, A.H.-J. | Citation | Journal: Biochemistry / Year: 2000 | Title: Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms. Authors: Yang, X.L. / Robinson, H. / Gao, Y.G. / Wang, A.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fdg.cif.gz | 15.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fdg.ent.gz | 10.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fdg ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fdg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA moleclue / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | ChemComp-9TA / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.67 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, sodium cacodylate buffer, magnesium chloride, cobalt chloride, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.7251 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 28, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7251 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→80 Å / Num. all: 57036 / Num. obs: 57036 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.523 / Num. unique all: 423 / % possible all: 99.5 |
Reflection | *PLUS Num. obs: 4270 / Num. measured all: 57036 |
-Processing
Software |
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Refinement | Resolution: 1.6→20 Å / σ(F): 4 / σ(I): 2 Stereochemistry target values: G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, H.M.BERMAN
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / σ(I): 2 / σ(F): 4 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 1.7 |