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Yorodumi- PDB-7dq0: Crystal structure of actinomycin D-echinomycin-d(ACGTGCT/AGCTCGT)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dq0 | ||||||||||||
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Title | Crystal structure of actinomycin D-echinomycin-d(ACGTGCT/AGCTCGT) complex | ||||||||||||
Components |
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Keywords | ANTIBIOTIC/DNA / Drug-DNA complex / DNA mismatch / DNA unwinding / DNA deformation / DNA / ANTIBIOTIC-DNA complex | ||||||||||||
Function / homology | Actinomycin D / Echinomycin / 2-CARBOXYQUINOXALINE / : / : / DNA Function and homology information | ||||||||||||
Biological species | Streptomyces sp. (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Satange, R.B. / Hou, M.H. | ||||||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects. Authors: Satange, R. / Chang, C.C. / Li, L.Y. / Lin, S.H. / Neidle, S. / Hou, M.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dq0.cif.gz | 28.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dq0.ent.gz | 16.7 KB | Display | PDB format |
PDBx/mmJSON format | 7dq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dq0_validation.pdf.gz | 464.9 KB | Display | wwPDB validaton report |
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Full document | 7dq0_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | 7dq0_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 7dq0_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/7dq0 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/7dq0 | HTTPS FTP |
-Related structure data
Related structure data | 7dq8C 1mnvS 5ytzS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-DNA (5'-D(P*AP*GP*CP*TP*CP*GP*T)- ... , 2 types, 2 molecules AB
#1: DNA chain | Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein/peptide , 2 types, 2 molecules CD
-Non-polymers , 4 types, 31 molecules
#5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 174.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O2 Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. References: Echinomycin #8: Water | ChemComp-HOH / | |
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-Details
Compound details | ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCI |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.38 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.5 mM Sodium Cacodylate, 1 mM Magnesium chloride, 1 mM Spermine tetrahydrochloride, 1.5 mM Zinc Chloride, 1% PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 19, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→30 Å / Num. obs: 7257 / % possible obs: 98.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.012 / Rrim(I) all: 0.035 / Χ2: 0.831 / Net I/σ(I): 12.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YTZ, 1MNV Resolution: 2→25.22 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.66 / Stereochemistry target values: ML Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.57 Å2 / Biso mean: 28.3076 Å2 / Biso min: 11.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→25.22 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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