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Open data
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Basic information
Entry | Database: PDB / ID: 7qce | |||||||||
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Title | Crystal structure of an atypical PHD finger of VIN3 | |||||||||
![]() | VIN3 (Protein VERNALIZATION INSENSITIVE 3) | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Franco-Echevarria, E. / Fiedler, M. / Dean, C. / Bienz, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Plant vernalization proteins contain unusual PHD superdomains without histone H3 binding activity. Authors: Franco-Echevarria, E. / Rutherford, T.J. / Fiedler, M. / 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 | ![]() | 145.8 KB | Display | ![]() |
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PDB format | ![]() | 116.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23225.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion Details: 0.06M Morpheus Divalents, 1.1M Morpheus Buffer System pH 6.5, 10% PEG 20K, 20% PEG 500 MME |
-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: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→50.84 Å / Num. obs: 27349 / % possible obs: 100 % / Redundancy: 19.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 2183 / CC1/2: 0.81 |
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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: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.149 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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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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