[English] 日本語
Yorodumi- PDB-8oex: Crystal structure of the native Z-DNA duplex d(CGCGCG) before soa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oex | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the native Z-DNA duplex d(CGCGCG) before soaking of CuCl2 | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA | Function / homology | SPERMINE / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.07 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 | 8oex.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8oex.ent.gz | 23.5 KB | Display | PDB format |
PDBx/mmJSON format | 8oex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oex_validation.pdf.gz | 381.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8oex_full_validation.pdf.gz | 381.5 KB | Display | |
Data in XML | 8oex_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 8oex_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/8oex ftp://data.pdbj.org/pub/pdb/validation_reports/oe/8oex | HTTPS FTP |
-Related structure data
Related structure data | 8oe7C 8oe8C 8oe9C 8oeaC 8oebC 8oecC 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: (0.200254449754, 0.978359251498, 0.0520704365433), (0.978406403649, -0.202474560624, 0.0415326570081), (0.0511767979838, 0.0426289491788, -0.997779388462)Vector: 3. ...NCS oper: (Code: given Matrix: (0.200254449754, 0.978359251498, 0.0520704365433), 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: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density % sol: 25.44 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: oligo, 2-methyl-2,4-pentanediol (MPD), sodium cacodylate, pH 6.0, KCl, NaCl and spermine tetrachloride |
-Data collection
Diffraction | Mean temperature: 100 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: Sep 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→18.28 Å / Num. obs: 10952 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 4.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.077 / Rrim(I) all: 0.199 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.07→1.09 Å / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 480 / CC1/2: 0.868 / Rpim(I) all: 0.241 / Rrim(I) all: 0.606 / % possible all: 92.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→17.48 Å / SU ML: 0.0553 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 10.9522 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: 8.27 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→17.48 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.870690915951 Å | ||||||||||||||||||||||||||||
LS refinement shell |
|