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- PDB-7o6t: Crystal structure of the polymerising VEL domain of VIN3 (R556D I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o6t | |||||||||
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Title | Crystal structure of the polymerising VEL domain of VIN3 (R556D I575D mutant) | |||||||||
![]() | (Protein VERNALIZATION INSENSITIVE 3) x 2 | |||||||||
![]() | NUCLEAR PROTEIN / protein oligomerization / head-to-tail polymerization / domain swapping | |||||||||
Function / homology | ![]() vernalization response / chromatin silencing complex / cellular response to cold / negative regulation of gene expression, epigenetic / response to cold / response to hypoxia / nuclear speck / DNA binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fiedler, M. / Franco-Echevarria, E. / Dean, C. / Bienz, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control. Authors: Fiedler, M. / Franco-Echevarria, E. / Schulten, A. / Nielsen, M. / Rutherford, T.J. / Yeates, A. / Ahsan, B. / Dean, C. / Bienz, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.6 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7o6uC ![]() 7o6vC ![]() 7o6wC ![]() 7oqvC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 8725.775 Da / Num. of mol.: 1 / Mutation: R556D I575D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 8649.657 Da / Num. of mol.: 1 / Mutation: R556D I575D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.06M Morpheus Divalents, 0.1M Morpheus Buffer System 2 pH 7.5, 10% w/v PEG 8K, 20% v/v ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→29.49 Å / Num. obs: 9677 / % possible obs: 99.7 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 2.02→2.07 Å / Num. unique obs: 677 / CC1/2: 0.93 |
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Processing
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Refinement | Method to determine structure: ![]() Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.648 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.069 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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