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Yorodumi- PDB-5u6z: Crystal Structure of Xenopus laevis Apex2 C-terminal Znf-GRF Domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u6z | ||||||
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Title | Crystal Structure of Xenopus laevis Apex2 C-terminal Znf-GRF Domain | ||||||
Components | DNA-(apurinic or apyrimidinic site) lyaseDNA-(apurinic or apyrimidinic site) lyase | ||||||
Keywords | LYASE / GRF Zinc Finger / 3' AP Endo/Exonuclease / DNA binding | ||||||
Function / homology | Function and homology information endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / mitochondrion / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Wallace, B.D. / Williams, R.S. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress. Authors: Wallace, B.D. / Berman, Z. / Mueller, G.A. / Lin, Y. / Chang, T. / Andres, S.N. / Wojtaszek, J.L. / DeRose, E.F. / Appel, C.D. / London, R.E. / Yan, S. / Williams, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u6z.cif.gz | 27.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u6z.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 5u6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/5u6z ftp://data.pdbj.org/pub/pdb/validation_reports/u6/5u6z | HTTPS FTP |
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-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
#1: Protein | Mass: 8272.509 Da / Num. of mol.: 1 / Fragment: residues 446-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: apex2, apex2-prov / Production host: Escherichia coli (E. coli) References: UniProt: Q6DDT4, DNA-(apurinic or apyrimidinic site) lyase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 61.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8 M (NH4)2SO4, 0.1 M Bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.28257 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 28, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.28257 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 5570 / % possible obs: 97.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 56.07 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→45.166 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 29.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.73 Å2 / Biso mean: 43.12 Å2 / Biso min: 28.97 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→45.166 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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