+Open data
-Basic information
Entry | Database: PDB / ID: 3cg7 | ||||||
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Title | Crystal structure of cell-death related nuclease 4 (CRN-4) | ||||||
Components | Cell death-related nuclease 4 | ||||||
Keywords | HYDROLASE / APOPTOSIS / 3'-5' exonuclease / DEDDh / nuclease | ||||||
Function / homology | Function and homology information DNA nuclease activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / apoptotic DNA fragmentation / DNA catabolic process / RNA catabolic process / RNA nuclease activity / 3'-5' exonuclease activity / DNA endonuclease activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity ...DNA nuclease activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / apoptotic DNA fragmentation / DNA catabolic process / RNA catabolic process / RNA nuclease activity / 3'-5' exonuclease activity / DNA endonuclease activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Hsiao, Y.-Y. / Yuan, H.S. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2009 Title: Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation Authors: Hsiao, Y.-Y. / Nakagawa, A. / Shi, Z. / Mitani, S. / Xue, D. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cg7.cif.gz | 243 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cg7.ent.gz | 197.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/3cg7 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/3cg7 | HTTPS FTP |
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-Related 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: 35592.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: crn-4 / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q10905, Hydrolases; Acting on ester bonds #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.84 Å3/Da / Density % sol: 74.61 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: 0.2M sodium formate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.50 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.5→30 Å / Num. obs: 45644 / % possible obs: 96.3 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rsym value: 0.052 / Net I/σ(I): 21.5 | ||||||||||||||||||
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.01 / Rsym value: 0.426 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.373 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.021 Å2
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Refine analyze | Luzzati coordinate error obs: 0.344 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.567 Å / Total num. of bins used: 20
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