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- PDB-4dnv: Crystal structure of the W285F mutant of UVB-resistance protein UVR8 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dnv | ||||||
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Title | Crystal structure of the W285F mutant of UVB-resistance protein UVR8 | ||||||
![]() | AT5g63860/MGI19_6 | ||||||
![]() | GENE REGULATION / WD40 Repeats / UV-B perception / COP1 | ||||||
Function / homology | ![]() entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding ...entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, D. / Hu, Q. / Yan, Z. / Chen, W. / Yan, C. / Zhang, J. / Wang, J. / Shi, Y. | ||||||
![]() | ![]() Title: Structural basis of ultraviolet-B perception by UVR8. Authors: Wu, D. / Hu, Q. / Yan, Z. / Chen, W. / Yan, C. / Huang, X. / Zhang, J. / Yang, P. / Deng, H. / Wang, J. / Deng, X. / Shi, 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 | ![]() | 570.6 KB | Display | ![]() |
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PDB format | ![]() | 475.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 477 KB | Display | |
Data in XML | ![]() | 59.2 KB | Display | |
Data in CIF | ![]() | 83.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dnuSC ![]() 4dnwC S: Starting model for refinement C: citing same article ( |
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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: 39836.332 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 12-381 / Mutation: W285F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 17%(w/v) PEG 8000, 100mM Tris pH8.5, 200mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.999→40 Å / Num. all: 82487 / Num. obs: 77456 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.999→2.07 Å / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DNU Resolution: 1.999→33.016 Å / SU ML: 0.48 / σ(F): 1.96 / Phase error: 27.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.48 Å2 / ksol: 0.318 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.999→33.016 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
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Refinement TLS params. | Method: refined / Origin x: 26.2165 Å / Origin y: 6.1229 Å / Origin z: 57.6135 Å
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Refinement TLS group | Selection details: ALL |