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Yorodumi- PDB-7x97: Crystal structure of actinomycin D-echinomycin-d(AGCCCGT/ACGGGCT)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x97 | ||||||||||||
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Title | Crystal structure of actinomycin D-echinomycin-d(AGCCCGT/ACGGGCT) complex | ||||||||||||
Components |
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Keywords | DNA/ANTIBIOTIC / C:G Watson-Crick base pair / Single-strand DNA twisting / Actinomycin D / Echinomycin / DNA-antibiotic complex / DNA | ||||||||||||
Function / homology | Actinomycin D / Echinomycin / : / 2-CARBOXYQUINOXALINE / DNA Function and homology information | ||||||||||||
Biological species | Streptomyces (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||
Authors | Kao, S.H. / Satange, R.B. / Hou, M.H. | ||||||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism. Authors: Satange, R. / Kao, S.H. / Chien, C.M. / Chou, S.H. / Lin, C.C. / 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 | 7x97.cif.gz | 39.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x97.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 7x97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x97_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 7x97_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | 7x97_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 7x97_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/7x97 ftp://data.pdbj.org/pub/pdb/validation_reports/x9/7x97 | HTTPS FTP |
-Related structure data
Related structure data | 7x6rC 7x9fC 7xdjC 7dq0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 chain , 2 types, 2 molecules AB
#1: DNA chain | Mass: 2098.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein/peptide , 2 types, 2 molecules GC
-Non-polymers , 5 types, 36 molecules
#5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-K / | #7: Chemical | #8: Chemical | #9: 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: 2.93 Å3/Da / Density % sol: 58.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.25 mM Oligonucleotides, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate (pH 6.5), 0.5 mM Spermine tetrahydrochloride, 6 mM Zinc chloride, 3.5 mM Potassium chloride, ...Details: 0.25 mM Oligonucleotides, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate (pH 6.5), 0.5 mM Spermine tetrahydrochloride, 6 mM Zinc chloride, 3.5 mM Potassium chloride, PEG200 3% (v/v), Reservoir PEG 200 (30% v/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 7161 / % possible obs: 97.8 % / Redundancy: 12.3 % / Biso Wilson estimate: 19.74 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.018 / Rrim(I) all: 0.06 / Χ2: 0.888 / Net I/σ(I): 7.7 / Num. measured all: 76141 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.399 / Num. unique obs: 702 / CC1/2: 0.999 / Rpim(I) all: 0.01 / Rrim(I) all: 0.034 / Χ2: 0.859 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DQ0 Resolution: 1.95→25.57 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.61 / Stereochemistry target values: ML
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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: 116.56 Å2 / Biso mean: 25.47 Å2 / Biso min: 7.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→25.57 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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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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