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Open data
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Basic information
Entry | Database: PDB / ID: 5dk5 | ||||||
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Title | Crystal structure of CRN-4-MES complex | ||||||
![]() | Cell death-related nuclease 4 | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() 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) / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsiao, Y.-Y. / Yuan, H.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of Inhibitors for the DEDDh Family of Exonucleases and a Unique Inhibition Mechanism by Crystal Structure Analysis of CRN-4 Bound with 2-Morpholin-4-ylethanesulfonate (MES) Authors: Huang, K.-W. / Hsu, K.-C. / Chu, L.-Y. / Yang, J.-M. / Yuan, H.S. / Hsiao, Y.-Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 373 KB | Display | ![]() |
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PDB format | ![]() | 320.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 314.3 KB | Display | ![]() |
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Full document | ![]() | 317.2 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cg7S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35592.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q10905, ![]() |
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-Non-polymers , 5 types, 465 molecules 








#2: Chemical | #3: Chemical | ![]() #4: Chemical | #5: Chemical | ChemComp-IPA / ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.66 % / Description: Rectangular columns |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50mM MES monohydrate, 20mM Magnesium chloride hexahydrate, 15%(v/v) 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→30 Å / Num. obs: 47266 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.33 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.12 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3CG7 Resolution: 2.1→29.751 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 20.25 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.751 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: -12.5884 Å / Origin y: -4.7919 Å / Origin z: 18.6382 Å
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Refinement TLS group | Selection details: all |