[English] 日本語
Yorodumi- PDB-8oec: Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordere... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oec | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for another 30 minutes, third collection at room temperature | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA | Function / homology | COPPER (II) ION / SPERMINE / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | Authors | Lambert, M.C. / Hall, J.P. | Funding support | United Kingdom, 1items |
Citation | Journal: To Be Published | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8oec.cif.gz | 25.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8oec.ent.gz | 13.7 KB | Display | PDB format |
PDBx/mmJSON format | 8oec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oec_validation.pdf.gz | 547.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8oec_full_validation.pdf.gz | 547.5 KB | Display | |
Data in XML | 8oec_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 8oec_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/8oec ftp://data.pdbj.org/pub/pdb/validation_reports/oe/8oec | HTTPS FTP |
-Related structure data
Related structure data | 8oe7C 8oe8C 8oe9C 8oeaC 8oebC 8oexC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
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: |
-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 | ChemComp-CU / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.85 % |
---|---|
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 |
---|---|
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: 2.1→17.65 Å / Num. obs: 1612 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 15.94 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.1→2.25 Å / Num. unique obs: 285 / CC1/2: 0.982 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→17.65 Å / SU ML: 0.0912 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.5244 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.34 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→17.65 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.513024023792 Å | ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→17.65 Å
|