[English] 日本語
Yorodumi- PDB-8a2v: Room temperature structure of the ground state of AtPhot2LOV2 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a2v | ||||||
---|---|---|---|---|---|---|---|
Title | Room temperature structure of the ground state of AtPhot2LOV2 in space group P43212 | ||||||
Components | Phototropin-2 | ||||||
Keywords | PLANT PROTEIN / LOV domain | ||||||
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 / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Engilberge, S. / Caramello, N. / Royant, A. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Iucrj / Year: 2022 Title: Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature. Authors: Aumonier, S. / Engilberge, S. / Caramello, N. / von Stetten, D. / Gotthard, G. / Leonard, G.A. / Mueller-Dieckmann, C. / Royant, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8a2v.cif.gz | 44.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8a2v.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 8a2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a2v_validation.pdf.gz | 754.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8a2v_full_validation.pdf.gz | 754.9 KB | Display | |
Data in XML | 8a2v_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 8a2v_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/8a2v ftp://data.pdbj.org/pub/pdb/validation_reports/a2/8a2v | HTTPS FTP |
-Related structure data
Related structure data | 8a2wC 8a4eC 6qqkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 |
---|---|
#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-MES / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.3 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES pH 6.0, 4 to 9 % PEG8000, and 50 to 200 mM calcium acetate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→34.78 Å / Num. obs: 14046 / % possible obs: 92.1 % / Redundancy: 8 % / CC1/2: 0.99 / Rpim(I) all: 0.071 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.59→1.64 Å / % possible obs: 46.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 297 / CC1/2: 0.58 / Rpim(I) all: 0.537 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QQK Resolution: 1.59→30.01 Å / Cross valid method: THROUGHOUT
| ||||||||||||||||||
Displacement parameters | Biso max: 120.98 Å2 / Biso mean: 23.7295 Å2 / Biso min: 7.93 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→30.01 Å
|