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Yorodumi- PDB-6tc5: Phytochromobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tc5 | ||||||
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Title | Phytochromobilin-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 / phosphorelay sensor kinase activity / photoreceptor 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: 2.1 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 | 6tc5.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tc5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/6tc5 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tc5 | HTTPS FTP |
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-Related structure data
Related structure data | 6tbySC 6tc7C 6tl4C 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
#1: Protein | Mass: 38904.570 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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#2: Chemical | ChemComp-O6E / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.68 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion / 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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.82 Å / Num. obs: 28169 / % possible obs: 99.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 38.875 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.088 / Rrim(I) all: 0.175 / Χ2: 1 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2275 / CC1/2: 0.536 / Rpim(I) all: 0.933 / Rrim(I) all: 1.873 / Χ2: 0.98 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TBY Resolution: 2.1→43.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.099 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.154 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: 38.875 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→43.82 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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