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- PDB-6qsa: Cryogenic temperature structure of blue light-irradiated AtPhot2L... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qsa | ||||||
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Title | Cryogenic temperature structure of blue light-irradiated AtPhot2LOV2 recorded after an accumulated dose of 48 kGy | ||||||
![]() | Phototropin-2 | ||||||
![]() | PLANT PROTEIN / Room temperature macromolecular crystallography / cryo-crystallography / specific radiation damage / time-resolved crystallography | ||||||
Function / homology | ![]() chloroplast relocation / : / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity ...chloroplast relocation / : / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aumonier, S. / Gotthard, G. / Royant, A. | ||||||
![]() | ![]() Title: Specific radiation damage is a lesser concern at room temperature. Authors: Gotthard, G. / Aumonier, S. / De Sanctis, D. / Leonard, G. / von Stetten, D. / Royant, A. #1: ![]() Title: Specific radiation damage is a lesser concern at room temperature Authors: Gotthard, G. / Aumonier, S. / De Sanctis, D. / Leonard, G. / von Stetten, D. / Royant, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.2 KB | Display | ![]() |
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PDB format | ![]() | 30.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qq8C ![]() 6qq9C ![]() 6qqaC ![]() 6qqbC ![]() 6qqcC ![]() 6qqdC ![]() 6qqeC ![]() 6qqfC ![]() 6qqhC ![]() 6qqiC ![]() 6qqjC ![]() 6qqkC ![]() 4eepS 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: 15007.909 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P93025, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 12-17% PEG8000 0.2 M Calcium Acetate 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.55 Å / Num. obs: 12659 / % possible obs: 99.8 % / Redundancy: 6.24 % / Biso Wilson estimate: 29.08 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.39 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.45 % / Mean I/σ(I) obs: 1.73 / Num. unique obs: 1199 / CC1/2: 0.791 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EEP Resolution: 1.7→38.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.791 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.729 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→38.55 Å
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Refine LS restraints |
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