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Open data
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Basic information
Entry | Database: PDB / ID: 4ct5 | ||||||
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Title | DDX6 | ||||||
![]() | DDX6 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body ...mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body / neuron differentiation / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ozgur, S. / Basquin, J. / Conti, E. | ||||||
![]() | ![]() Title: Structural and Biochemical Insights to the Role of the Ccr4-not Complex and Ddx6 ATPase in Microrna Repression. Authors: Mathys, H. / Basquin, J. / Ozgur, S. / Czarnocki-Cieciura, M. / Bonneau, F. / Aartse, A. / Dziembowski, A. / Nowotny, M. / Conti, E. / Filipowicz, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 279.4 KB | Display | ![]() |
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PDB format | ![]() | 228.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.6 KB | Display | ![]() |
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Full document | ![]() | 451.5 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ct4C ![]() 4ct6C ![]() 4ct7C ![]() 4cv5C ![]() 2waxS 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: 43189.195 Da / Num. of mol.: 2 / Fragment: RECA1, RECA2, RESIDUES 95-469 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | Sequence details | THE FIRST 3 AMINO ACIDS ARE FROM THE PROTEASE CLEAVAGE SITE (RSM) | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 17% (W/V) PEG 10000, 100 MM BIS-TRIS PH 5.5 AND 100 MM AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 3→80 Å / Num. obs: 27769 / % possible obs: 99.4 % / Observed criterion σ(I): 2.4 / Redundancy: 5.2 % / Biso Wilson estimate: 81.79 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3→3.17 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WAX Resolution: 3→50.59 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 34.31 / 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: 3→50.59 Å
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Refine LS restraints |
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LS refinement shell |
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