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Yorodumi- PDB-6tby: Phycocyanobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tby | ||||||
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Title | Phycocyanobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB | ||||||
Components | Phytochrome | ||||||
Keywords | PLANT PROTEIN / phytochrome | ||||||
Function / homology | Function and homology information protein-phytochromobilin linkage / red, far-red light phototransduction / detection of visible light / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Sorghum bicolor (sorghum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Nagano, S. / Guan, K. / Shenkutie, S.M. / Hughes, J.E. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat.Plants / Year: 2020 Title: Structural insights into photoactivation and signalling in plant phytochromes. Authors: Nagano, S. / Guan, K. / Shenkutie, S.M. / Feiler, C. / Weiss, M. / Kraskov, A. / Buhrke, D. / Hildebrandt, P. / Hughes, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tby.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tby.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tby_validation.pdf.gz | 805.3 KB | Display | wwPDB validaton report |
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Full document | 6tby_full_validation.pdf.gz | 810.2 KB | Display | |
Data in XML | 6tby_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 6tby_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tby ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tby | HTTPS FTP |
-Related structure data
Related structure data | 6tc5C 6tc7C 6tl4C 4ourS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 38889.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: PHYB, SORBI_3001G394400 / Plasmid: pPROLar.A122 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6S527, UniProt: P93527*PLUS |
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-Non-polymers , 5 types, 151 molecules
#2: Chemical | ChemComp-CYC / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.14 Å3/Da / Density % sol: 60.85 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: (100 mM Tris/HCl pH 8.5, 500 mM NaCl, 9% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.1 Å / Num. obs: 44840 / % possible obs: 99.4 % / Redundancy: 20.3 % / Biso Wilson estimate: 39.819 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.026 / Rrim(I) all: 0.086 / Χ2: 0.98 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 21.3 % / Rmerge(I) obs: 2.726 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2647 / CC1/2: 0.646 / Rpim(I) all: 0.858 / Rrim(I) all: 2.858 / Χ2: 0.88 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OUR Resolution: 1.8→44.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.633 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.098 Details: Hydrogens have been added in their 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: 39.819 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.1 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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