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Open data
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Basic information
Entry | Database: PDB / ID: 4qn0 | ||||||
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Title | Crystal structure of the CPS-6 mutant Q130K | ||||||
![]() | Endonuclease G, mitochondrial | ||||||
![]() | HYDROLASE / beta-beta-alpha metal motif / endoribonuclease / mitochondrial membrane | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / double-stranded DNA endonuclease activity / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / RNA catabolic process / RNA endonuclease activity / DNA endonuclease activity / endonuclease activity / sequence-specific DNA binding ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / double-stranded DNA endonuclease activity / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / RNA catabolic process / RNA endonuclease activity / DNA endonuclease activity / endonuclease activity / sequence-specific DNA binding / mitochondrial inner membrane / protein homodimerization activity / mitochondrion / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, J.L.J. / Yuan, H.S. | ||||||
![]() | ![]() Title: Oxidative Stress Impairs Cell Death by Repressing the Nuclease Activity of Mitochondrial Endonuclease G Authors: Lin, J.L.J. / Nakagawa, A. / Skeen-Gaar, R. / Yang, W.Z. / Zhao, P. / Zhang, Z. / Ge, X. / Mitani, S. / Xue, D. / Yuan, H.S. #1: ![]() Title: Structural Insights into Apoptotic DNA Degradation by CED-3 Protease Suppressor-6 (CPS-6) from Caenorhabditis elegans Authors: Lin, J.L.J. / Nakagawa, A. / Hsiao, Y.Y. / Yang, W.Z. / Wang, Y.T. / Doudeva, L.G. / Skeen-Gaar, R.R. / Xui, D. / Yuan, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.6 KB | Display | ![]() |
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PDB format | ![]() | 162.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
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Full document | ![]() | 458.8 KB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 49.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s5bS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27397.334 Da / Num. of mol.: 4 / Fragment: UNP residues 64-302 / Mutation: H148A, Q130K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q95NM6, 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 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M sodium citrate tribasic dihydrate, 18% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 8, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.74→26.48 Å / Num. all: 29545 / Num. obs: 29545 / % possible obs: 99.7 % / Observed criterion σ(I): 4.26 / Redundancy: 3.7 % / Biso Wilson estimate: 27.42 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.077 / Net I/σ(I): 11.49 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3S5B Resolution: 2.74→26.48 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 24.34 / Stereochemistry target values: ML
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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: 35.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→26.48 Å
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Refine LS restraints |
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LS refinement shell |
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