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- PDB-5svu: Structure and kinetics of the LOV domain of ZEITLUPE determine it... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5svu | ||||||
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Title | Structure and kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis | ||||||
![]() | Adagio protein 1 | ||||||
![]() | CIRCADIAN CLOCK PROTEIN / LOV / Kinetics / PAS domain / photoreceptor | ||||||
Function / homology | ![]() response to blue light / flower development / SCF ubiquitin ligase complex / photoreceptor activity / circadian rhythm / protein ubiquitination / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zoltowski, B. / Pudasaini, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Kinetics of the LOV domain of ZEITLUPE determine its circadian function inArabidopsis. Authors: Pudasaini, A. / Shim, J.S. / Song, Y.H. / Shi, H. / Kiba, T. / Somers, D.E. / Imaizumi, T. / Zoltowski, B.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.7 KB | Display | ![]() |
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PDB format | ![]() | 166.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5svgC ![]() 5svvC ![]() 5svwC ![]() 3d72S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15394.649 Da / Num. of mol.: 4 / Fragment: LOV domain (UNP residues 29-165) / Mutation: G80R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FMN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 0.2 M Magnesium Chloride hexahydrate, 30% w/v PEG 4k |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 26153 / % possible obs: 97.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 55.4 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 7.8 / % possible all: 86.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3D72 Resolution: 2.601→49.506 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.74 / 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: 2.601→49.506 Å
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Refine LS restraints |
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LS refinement shell |
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