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Yorodumi- PDB-8a2w: Room temperature structure of the ground state of AtPhot2LOV2 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a2w | ||||||
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Title | Room temperature structure of the ground state of AtPhot2LOV2 in space group P212121, as recovered 1620 seconds after light irradiation | ||||||
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: 2.04 Å | ||||||
Authors | Engilberge, S. / Caramello, N. / Royant, A. | ||||||
Funding support | 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a2w.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a2w.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 8a2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a2w_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8a2w_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8a2w_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 8a2w_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/8a2w ftp://data.pdbj.org/pub/pdb/validation_reports/a2/8a2w | HTTPS FTP |
-Related structure data
Related structure data | 8a2vC 8a4eC 6qqkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 15007.909 Da / Num. of mol.: 2 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 | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 36.34 % |
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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 |
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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: 2.04→34.51 Å / Num. obs: 10070 / % possible obs: 78 % / Redundancy: 4 % / CC1/2: 0.98 / Rpim(I) all: 0.089 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.04→2.11 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 504 / CC1/2: 0.49 / Rpim(I) all: 0.569 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QQK Resolution: 2.04→34.51 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.08 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.56 Å2 / Biso mean: 42.6074 Å2 / Biso min: 15.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→34.51 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Origin x: 7.6951 Å / Origin y: 2.5338 Å / Origin z: 16.7292 Å
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Refinement TLS group |
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