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- PDB-8oeb: Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordere... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8oeb | ||||||||||||||||||||||||||||
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Title | Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for 30 minutes, second collection at room temperature | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA | Function / homology | COPPER (II) ION / SPERMINE / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() Lambert, M.C. / Hall, J.P. | Funding support | | ![]()
![]() ![]() Title: Structural analysis of peroxide-soaked DNA crystals containing ordered copper binding sites: towards understanding oxidative damage at the atomic scale Authors: Lambert, M.C. / Hall, J.P. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 31.9 KB | Display | ![]() |
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PDB format | ![]() | 19.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1022 KB | Display | ![]() |
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Full document | ![]() | 1022 KB | Display | |
Data in XML | ![]() | 3.1 KB | Display | |
Data in CIF | ![]() | 3.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oe7C ![]() 8oe8C ![]() 8oe9C ![]() 8oeaC ![]() 8oecC ![]() 8oexC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.223088265613, 0.973125932262, 0.0570749130893), (0.972127118702, -0.226426787544, 0.0608257755157), (0.0721144287245, 0.0419145540473, -0.996515267986)Vector: 3. ...NCS oper: (Code: given Matrix: (0.223088265613, 0.973125932262, 0.0570749130893), Vector: |
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Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SPM / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: oligo, 2-methyl-2,4-pentanediol (MPD), sodium cacodylate, KCl, NaCl and spermine tetrachloride |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5406 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→18.31 Å / Num. obs: 2494 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 14.11 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.8→1.88 Å / Num. unique obs: 294 / CC1/2: 0.952 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 16.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→17.67 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.580486504008 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→17.67 Å
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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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