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Open data
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Basic information
Entry | Database: PDB / ID: 6lyf | ||||||
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Title | Crystal structure of the mouse endonuclease EndoG(H138A/Se-Met) | ||||||
![]() | Endonuclease G, mitochondrial | ||||||
![]() | APOPTOSIS / EndoG / DNase / mitochondria | ||||||
Function / homology | ![]() mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of mitochondrial DNA replication / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA nuclease activity / positive regulation of apoptotic DNA fragmentation / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / negative regulation of TOR signaling ...mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of mitochondrial DNA replication / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA nuclease activity / positive regulation of apoptotic DNA fragmentation / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / negative regulation of TOR signaling / response to tumor necrosis factor / positive regulation of autophagy / RNA endonuclease activity / DNA endonuclease activity / perikaryon / in utero embryonic development / nucleic acid binding / mitochondrial inner membrane / positive regulation of apoptotic process / response to antibiotic / DNA damage response / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, K.H. / Woo, E.J. | ||||||
![]() | ![]() Title: Crystal structure of the mouse endonuclease G. Authors: Park, K.H. / Yoon, S.M. / Song, H.N. / Yang, J.H. / Ryu, S.E. / Woo, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 436 KB | Display | ![]() |
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PDB format | ![]() | 310.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 35.9 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 27598.734 Da / Num. of mol.: 4 / Mutation: H138A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O08600, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 200mM NaCl, 1mM CdCl2, 100mM CHES, 10mM CTAB, 5% glycerol, 5% MPD |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.12 Å / Num. obs: 56219 / % possible obs: 99.7 % / Redundancy: 14.3 % / Biso Wilson estimate: 39.44 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.8→2.85 Å / Num. unique obs: 28825 / Rsym value: 0.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.12 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.3241861153 Å / Origin y: 27.5101005381 Å / Origin z: 67.3070337233 Å
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Refinement TLS group | Selection details: all |