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Yorodumi- PDB-2z6d: Crystal structure of LOV1 domain of phototropin2 from Arabidopsis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6d | ||||||
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Title | Crystal structure of LOV1 domain of phototropin2 from Arabidopsis thaliana | ||||||
Components | Phototropin-2 | ||||||
Keywords | TRANSFERASE / PAS-fold / LOV-fold / Alternative splicing / ATP-binding / Chromophore / Flavoprotein / FMN / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Photoreceptor protein / Receptor / Sensory transduction / Serine/threonine-protein kinase | ||||||
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 / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Nakasako, M. / Matsuoka, D. / Tokutomi, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2 Authors: Nakasako, M. / Zikihara, K. / Matsuoka, D. / Katsura, H. / Tokutomi, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization and preliminary X-ray diffraction analysis of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana Authors: Nakasako, M. / Hirata, M. / Shimizu, N. / Hosokawa, S. / Matsuoka, D. / Oka, T. / Yamamoto, M. / Tokutomi, S. #2: Journal: Biochemistry / Year: 2004 Title: Light-induced structural changes of LOV domain-containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering Authors: Nakasako, M. / Iwata, T. / Matsuoka, D. / Tokutomi, S. #3: Journal: FEBS Lett. / Year: 2005 Title: Quaternary structure of LOV-domain containing polypeptide of Arabidopsis FKF1 protein Authors: Nakasako, M. / Matsuoka, D. / Zikihara, K. / Tokutomi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z6d.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6d.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 2z6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6d ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6d | HTTPS FTP |
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-Related structure data
Related structure data | 2z6cC 1n9lS 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: 14570.555 Da / Num. of mol.: 2 / Fragment: UNP residues 117-246, LOV1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT2, CAV1, KIN7, NPL1 / Production host: Escherichia coli (E. coli) References: UniProt: P93025, non-specific serine/threonine protein kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000, Sodium acetate, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2006 / Details: monochrometer/focusing optics |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→70 Å / Num. obs: 15677 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 6.59 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N9L Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.771 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.892 Å2
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.05 Å / Total num. of bins used: 20
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