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Yorodumi- PDB-6qqk: Room temperature structure of blue light-irradiated AtPhot2LOV2 r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qqk | ||||||
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Title | Room temperature structure of blue light-irradiated AtPhot2LOV2 recorded after an accumulated dose of 34 kGy | ||||||
Components | Phototropin-2 | ||||||
Keywords | PLANT PROTEIN / Room temperature macromolecular crystallography / cryo-crystallography / specific radiation damage / time-resolved crystallography | ||||||
Function / homology | Function and homology information chloroplast relocation / negative regulation of anion channel activity by blue light / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity ...chloroplast relocation / negative regulation of anion channel activity by blue light / 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 / membrane / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Aumonier, S. / Gotthard, G. / Royant, A. | ||||||
Citation | Journal: Iucrj / Year: 2019 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: Journal: Iucrj / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qqk.cif.gz | 41.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qqk.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 6qqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/6qqk ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qqk | HTTPS FTP |
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-Related structure data
Related structure data | 6qq8C 6qq9C 6qqaC 6qqbC 6qqcC 6qqdC 6qqeC 6qqfC 6qqhC 6qqiC 6qqjC 6qsaC 4eepS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Arabidopsis thaliana (thale cress) / Gene: PHOT2, CAV1, KIN7, NPL1, At5g58140, K21L19.6 / Production host: Escherichia coli BL21(DE3) (bacteria) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.63 % |
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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: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.59 Å / Num. obs: 4926 / % possible obs: 98 % / Redundancy: 23.1 % / Biso Wilson estimate: 51.997 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.64 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 23.5 % / Mean I/σ(I) obs: 1.52 / Num. unique obs: 558 / CC1/2: 0.726 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4eep Resolution: 2.4→39.59 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.083 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.843 / ESU R Free: 0.332 / 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: 46.905 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→39.59 Å
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Refine LS restraints |
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