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Yorodumi- PDB-7n3z: Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n3z | ||||||
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Title | Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain | ||||||
Components | DNA-(apurinic or apyrimidinic site) endonuclease 2 | ||||||
Keywords | HYDROLASE / nuclease / DNA repair / EEP fold / APE2 homolog | ||||||
Function / homology | Function and homology information double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / base-excision repair / endonuclease activity / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Wojtaszek, J.L. / Wallace, B.D. / Williams, R.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2022 Title: Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2. Authors: Williams, J.S. / Wojtaszek, J.L. / Appel, D.C. / Krahn, J. / Wallace, B.D. / Walsh, E. / Kunkel, T.A. / 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 | 7n3z.cif.gz | 248.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n3z.ent.gz | 194.6 KB | Display | PDB format |
PDBx/mmJSON format | 7n3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n3z_validation.pdf.gz | 430.4 KB | Display | wwPDB validaton report |
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Full document | 7n3z_full_validation.pdf.gz | 431.5 KB | Display | |
Data in XML | 7n3z_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 7n3z_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/7n3z ftp://data.pdbj.org/pub/pdb/validation_reports/n3/7n3z | HTTPS FTP |
-Related structure data
Related structure data | 7n3yC 3g0rS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47324.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: APN2, ETH1, YBL019W, YBL0443 / Production host: Escherichia coli (E. coli) References: UniProt: P38207, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 25% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→36.67 Å / Num. obs: 26508 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.33 Å2 / Rrim(I) all: 0.107 / Net I/σ(I): 14.42 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.99 / Num. unique obs: 2254 / Rrim(I) all: 0.548 / % possible all: 83.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3g0r Resolution: 1.99→36.67 Å / SU ML: 0.1871 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.3319 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: 37.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→36.67 Å
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Refine LS restraints |
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LS refinement shell |
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