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Yorodumi- PDB-2d55: Structural, physical and biological characteristics of RNA.DNA bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d55 | |||||||||||||||
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Title | Structural, physical and biological characteristics of RNA.DNA binding agent N8-actinomycin D | |||||||||||||||
Components |
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Keywords | DNA/ANTIBIOTIC / ACTINOMYCIN D / DACTINOMYCIN / ANTIBIOTIC / ANTI CANCER / ANTITUMOR / CHROMOPHORE / DEPSIPEPTIDE / DNA-ANTIBIOTIC COMPLEX | |||||||||||||||
Function / homology | Actinomycin D / : / DNA Function and homology information | |||||||||||||||
Biological species | STREPTOMYCES ANTIBIOTICUS (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | |||||||||||||||
Authors | Shinomiya, M. / Chu, W. / Carlson, R.G. / Weaver, R.F. / Takusagawa, F. | |||||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Crystal Structure of the 2:1 Complex between D(Gaagcttc) and the Anticancer Drug Actinomycin D. Authors: Kamitori, S. / Takusagawa, F. #1: Journal: Biochemistry / Year: 1995 Title: Structural, Physical, and Biological Characteristics of RNA.DNA Binding Agent N8- Actinomycin D. Authors: Shinomiya, M. / Chu, W. / Carlson, R.G. / Weaver, R.F. / Takusagawa, F. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d55.cif.gz | 31.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d55.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 2d55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d55_validation.pdf.gz | 399.2 KB | Display | wwPDB validaton report |
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Full document | 2d55_full_validation.pdf.gz | 409.9 KB | Display | |
Data in XML | 2d55_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 2d55_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d55 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d55 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein/peptide | | Type: Polypeptide / Class: Antibiotic / Mass: 1291.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ) Source: (natural) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, Actinomycin D #3: Water | ChemComp-HOH / | Compound details | ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.32 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: PH 7.00, VAPOR DIFFUSION, TEMPERATURE 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Kamitori, S., (1992) J.Mol.Biol., 225, 445. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE |
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Detector | Detector: DIFFRACTOMETER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3→7 Å /
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Refinement step | Cycle: LAST / Resolution: 3→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 7 Å / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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