+Open data
-Basic information
Entry | Database: PDB / ID: 6k17 | ||||||
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Title | Crystal structure of EXD2 exonuclease domain | ||||||
Components | Exonuclease 3'-5' domain-containing protein 2 | ||||||
Keywords | HYDROLASE / 3'-5' exonuclease / DnaQ family | ||||||
Function / homology | Function and homology information exodeoxyribonuclease I / nucleic acid metabolic process / DNA double-strand break processing / single-stranded DNA 3'-5' DNA exonuclease activity / intermediate filament cytoskeleton / 3'-5'-DNA exonuclease activity / replication fork processing / site of DNA damage / 3'-5' exonuclease activity / double-strand break repair via homologous recombination ...exodeoxyribonuclease I / nucleic acid metabolic process / DNA double-strand break processing / single-stranded DNA 3'-5' DNA exonuclease activity / intermediate filament cytoskeleton / 3'-5'-DNA exonuclease activity / replication fork processing / site of DNA damage / 3'-5' exonuclease activity / double-strand break repair via homologous recombination / double-strand break repair / manganese ion binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial outer membrane / mitochondrial matrix / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å | ||||||
Authors | Park, J. / Lee, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination. Authors: Park, J. / Lee, S.Y. / Jeong, H. / Kang, M.G. / Van Haute, L. / Minczuk, M. / Seo, J.K. / Jun, Y. / Myung, K. / Rhee, H.W. / Lee, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k17.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k17.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 6k17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k17_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 6k17_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6k17_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 6k17_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/6k17 ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k17 | HTTPS FTP |
-Related structure data
Related structure data | 6k18C 6k19C 6k1aC 6k1bC 6k1cC 6k1dC 6k1eC 2fbtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24396.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EXD2, C14orf114, EXDL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVH0, exodeoxyribonuclease I #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: PEG 8000, 2-(N-morpholino)ethanesulfonic acid, Calcium acetate, Dithiothreitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 60416 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 22.54 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.715 / Num. unique obs: 2976 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FBT Resolution: 1.602→37.332 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.602→37.332 Å
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Refine LS restraints |
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LS refinement shell |
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