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- PDB-3krn: Crystal Structure of C. elegans cell-death-related nuclease 5(CRN-5) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3krn | ||||||
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Title | Crystal Structure of C. elegans cell-death-related nuclease 5(CRN-5) | ||||||
![]() | Protein C14A4.5, confirmed by transcript evidence | ||||||
![]() | HYDROLASE / RNase PH domain / homodimer / exosome / cell-death-related DNase | ||||||
Function / homology | GHMP Kinase, N-terminal domain / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, C.-C. / Wang, Y.-T. / Hsiao, Y.-Y. / Doudeva, L.G. / Chow, S.Y. / Yuan, H.S. | ||||||
![]() | ![]() Title: Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation Authors: Yang, C.-C. / Wang, Y.-T. / Hsiao, Y.-Y. / Doudeva, L.G. / Kuo, P.-H. / Chow, S.Y. / 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 | ![]() | 70 KB | Display | ![]() |
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PDB format | ![]() | 52.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hkmC ![]() 2nn6S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 24108.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q17952, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl, 0.2M NaCl, 25% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 102 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2008 |
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: 3.9→50 Å / Num. obs: 3235 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 66.08 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.091 / Net I/σ(I): 13.8 / Num. measured all: 9991 |
Reflection shell | Resolution: 3.9→4.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.25 / Num. unique all: 305 / Rsym value: 0.267 / % possible all: 91.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NN6, chain D Resolution: 3.918→26.505 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.627 / SU ML: 0.54 / Isotropic thermal model: overall / σ(F): 1.38 / Phase error: 41.02 / 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 / Bsol: 76.401 Å2 / ksol: 0.318 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 264.89 Å2 / Biso mean: 87.869 Å2 / Biso min: 11.83 Å2
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Refinement step | Cycle: LAST / Resolution: 3.918→26.505 Å
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Refine LS restraints |
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LS refinement shell |
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