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Yorodumi- PDB-1fd5: BINDING OF A MACROCYCLIC BISACRIDINE AND AMETANTRONE TO CGTACG IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fd5 | ||||||||||||||||||
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Title | BINDING OF A MACROCYCLIC BISACRIDINE AND AMETANTRONE TO CGTACG INVOLVES SIMILAR UNUSUAL INTERCALATION PLATFORMS (BISACRIDINE 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 | MACROCYCLIC-BIS-9-AMINO-ACRIDINE / : / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 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 | 1fd5.cif.gz | 26.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fd5.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fd5_validation.pdf.gz | 786.4 KB | Display | wwPDB validaton report |
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Full document | 1fd5_full_validation.pdf.gz | 789 KB | Display | |
Data in XML | 1fd5_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 1fd5_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fd5 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fd5 | HTTPS FTP |
-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 #2: Chemical | #3: Chemical | ChemComp-B9A / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.17 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.1→100 Å / Num. all: 196823 / Num. obs: 196823 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 40.5 | |||||||||||||||
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.597 / Num. unique all: 1293 / % possible all: 100 | |||||||||||||||
Reflection | *PLUS Num. obs: 13377 / Num. measured all: 196823 |
-Processing
Software |
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Refinement | Resolution: 1.1→10 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: 1.1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 10 Å / σ(I): 2 / σ(F): 4 / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 2 |