+Open data
-Basic information
Entry | Database: PDB / ID: 6tl4 | ||||||
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Title | Photosensory module (PAS-GAF-PHY) of Glycine max phyB | ||||||
Components | Phytochrome | ||||||
Keywords | PLANT PROTEIN / phytochrome | ||||||
Function / homology | Function and homology information protein-phycocyanobilin linkage / red, far-red light phototransduction / detection of visible light / : / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / protein homodimerization activity / nucleus Similarity search - Function | ||||||
Biological species | Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 6tl4.cif.gz | 251.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tl4.ent.gz | 170.9 KB | Display | PDB format |
PDBx/mmJSON format | 6tl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tl4_validation.pdf.gz | 767.9 KB | Display | wwPDB validaton report |
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Full document | 6tl4_full_validation.pdf.gz | 784.5 KB | Display | |
Data in XML | 6tl4_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 6tl4_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/6tl4 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/6tl4 | HTTPS FTP |
-Related structure data
Related structure data | 6tbyC 6tc5C 6tc7C 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
#1: Protein | Mass: 59896.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Gene: 100794865, GLYMA_15G140000 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I1MGE5 |
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#2: Chemical | ChemComp-CYC / |
#3: 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: 5.63 Å3/Da / Density % sol: 78.15 % / Description: Hexagonal bipyramid |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200mM MES, 200mM KSCN, 200mM LiCl2, 1% w/v gamma-PGA, 3% w/v PEG3350 |
-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 PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.17 Å / Num. obs: 30704 / % possible obs: 99.9 % / Redundancy: 19.8 % / Biso Wilson estimate: 85.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.238 / Rpim(I) all: 0.077 / Rrim(I) all: 0.251 / Χ2: 1.01 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 19.9 % / Rmerge(I) obs: 5.838 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4420 / CC1/2: 0.591 / Rpim(I) all: 1.893 / Rrim(I) all: 6.14 / Χ2: 1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OUR Resolution: 2.9→47.17 Å / SU ML: 0.4858 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4519
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 121.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→47.17 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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