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Yorodumi- PDB-7oqv: Crystal structure of the polymerising VEL domain of VIN3 (I575D m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oqv | |||||||||
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Title | Crystal structure of the polymerising VEL domain of VIN3 (I575D mutant) | |||||||||
Components | Protein VERNALIZATION INSENSITIVE 3 | |||||||||
Keywords | NUCLEAR PROTEIN / protein oligomerization / head-to-tail polymerization / domain swapping | |||||||||
Function / homology | Function and homology information 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 | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | |||||||||
Authors | Fiedler, M. / Franco-Echevarria, E. / Dean, C. / Bienz, M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Cell Rep / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oqv.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oqv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oqv_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 7oqv_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 7oqv_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 7oqv_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/7oqv ftp://data.pdbj.org/pub/pdb/validation_reports/oq/7oqv | HTTPS FTP |
-Related structure data
Related structure data | 7o6tC 7o6uC 7o6vC 7o6wC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8845.021 Da / Num. of mol.: 4 / Mutation: I575D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VIN3, At5g57380, MSF19.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FIE3 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 1M potassium phosphate monobasic, 3 % v/v 2 propanol, 0.1M sodium cacodylate pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
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: 2.4→29.07 Å / Num. obs: 11740 / % possible obs: 100 % / Redundancy: 8.7 % / CC1/2: 1 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 11740 / CC1/2: 0.91 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→29.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.826 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.647 / ESU R Free: 0.303 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.228 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.07 Å
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Refine LS restraints |
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LS refinement shell |
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