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Yorodumi- PDB-5yze: Crystal structure of the [Co2+-(chromomycin A3)2]-d(CCG)3 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yze | ||||||||||||||||||||||||||
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Title | Crystal structure of the [Co2+-(chromomycin A3)2]-d(CCG)3 complex | ||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | ANTIBIOTICS/DNA / Drug-DNA complex / Chromomycin A3 / CCG repeats / i-motif / flipout / DNA / ANTIBIOTICS-DNA complex | Function / homology | : / Chem-CPH / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.87 Å | Authors | Hou, M.H. / Chen, Y.W. / Wu, P.C. / Satange, R.B. | Citation | Journal: Int J Mol Sci / Year: 2018 | Title: CoII(Chromomycin)2 Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex Authors: Chen, Y.W. / Satange, R. / Wu, P.C. / Jhan, C.R. / Chang, C.K. / Chung, K.R. / Waring, M.J. / Lin, S.W. / Hsieh, L.C. / 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 | 5yze.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yze.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yze_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 5yze_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5yze_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 5yze_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/5yze ftp://data.pdbj.org/pub/pdb/validation_reports/yz/5yze | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 1 types, 2 molecules AB
#1: DNA chain | Mass: 3295.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 82 molecules
#4: Chemical | #5: Chemical | #6: 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: 3.64 Å3/Da / Density % sol: 66.22 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.75mM DNA, 1.5mM Chro, 3mM Cobalt, 50mM Sodium Cacodylate (pH= 6.0), 1mM MgCl2, 1% MPD eqillibriated against 30% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.56418 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2012 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.56418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→27.2 Å / Num. obs: 7726 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 31.27 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 44.55 |
Reflection shell | Resolution: 1.87→1.94 Å / Rmerge(I) obs: 0.171 / Num. unique obs: 775 / Rsym value: 0.171 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.87→27.18 Å / SU ML: 0.142 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 30.171
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→27.18 Å
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Refine LS restraints |
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LS refinement shell |
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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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