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Open data
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Basic information
Entry | Database: PDB / ID: 6k18 | ||||||
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Title | Crystal structure of EXD2 exonuclease domain soaked in Mn | ||||||
![]() | Exonuclease 3'-5' domain-containing protein 2 | ||||||
![]() | HYDROLASE / 3'-5' exonuclease / DnaQ family | ||||||
Function / homology | ![]() 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 / mitochondrial outer membrane / nucleic acid binding / mitochondrial matrix / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, J. / Lee, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.9 KB | Display | ![]() |
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PDB format | ![]() | 70.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k17SC ![]() 6k19C ![]() 6k1aC ![]() 6k1bC ![]() 6k1cC ![]() 6k1dC ![]() 6k1eC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % |
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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, Manganese chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 20317 / % possible obs: 98.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 12.35 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.348 / Num. unique obs: 939 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6K17 Resolution: 2.303→43.609 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 25.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.303→43.609 Å
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Refine LS restraints |
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LS refinement shell |
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