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Yorodumi- PDB-2z6c: Crystal structure of LOV1 domain of phototropin1 from Arabidopsis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6c | ||||||
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Title | Crystal structure of LOV1 domain of phototropin1 from Arabidopsis thaliana | ||||||
Components | Phototropin-1 | ||||||
Keywords | TRANSFERASE / PAS-FOLD / LOV-FOLD / ATP-binding / Chromophore / Cytoplasm / Flavoprotein / FMN / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Photoreceptor protein / Receptor / Sensory transduction / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information chloroplast avoidance movement / chloroplast accumulation movement / cellular response to blue light / regulation of proton transport / negative regulation of anion channel activity by blue light / phototropism / response to blue light / regulation of stomatal movement / blue light photoreceptor activity / plant-type vacuole ...chloroplast avoidance movement / chloroplast accumulation movement / cellular response to blue light / regulation of proton transport / negative regulation of anion channel activity by blue light / phototropism / response to blue light / regulation of stomatal movement / blue light photoreceptor activity / plant-type vacuole / cytoplasmic side of plasma membrane / circadian rhythm / FMN binding / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / cell surface / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 2z6c.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6c.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2z6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6c ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6c | HTTPS FTP |
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-Related structure data
Related structure data | 2z6dC 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: 14199.078 Da / Num. of mol.: 2 / Fragment: UNP residues 180-308, LOV1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT1, JK224, NPH1, RPT1 / Production host: Escherichia coli (E. coli) References: UniProt: O48963, 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: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, pH8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2007 / Details: monochrometer/focusing mirror |
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: 2.1→50 Å / Num. obs: 16967 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 13.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 41.8 |
Reflection shell | Resolution: 2.1→2.17 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.8 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N9L Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.128 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.187 / 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: 29.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Total num. of bins used: 20
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