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- PDB-8k9o: Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k9o | ||||||||||||
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Title | Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state | ||||||||||||
![]() | histidine kinase![]() | ||||||||||||
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Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Nagae, T. / Hirose, Y. / Mishima, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Green/red light-sensing mechanism in the chromatic acclimation photosensor Authors: Nagae, T. / Fujita, Y. / Tsuchida, T. / Kamo, T. / Seto, R. / Hamada, M. / Aoyama, H. / Sato-Tomita, A. / Fujisawa, T. / Eki, T. / Miyanoiri, Y. / Ito, Y. / Soeta, T. / Ukaji, Y. / Unno, M. ...Authors: Nagae, T. / Fujita, Y. / Tsuchida, T. / Kamo, T. / Seto, R. / Hamada, M. / Aoyama, H. / Sato-Tomita, A. / Fujisawa, T. / Eki, T. / Miyanoiri, Y. / Ito, Y. / Soeta, T. / Ukaji, Y. / Unno, M. / Mishima, M. / Hirose, Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.9 KB | Display | ![]() |
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PDB format | ![]() | 36.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ckvS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 22045.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CYC / ![]() |
#3: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.57 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, magnesium acetate, sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2022 |
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.75→45.489 Å / Num. obs: 18446 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Χ2: 0.98 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1002 / CC1/2: 0.876 / Χ2: 1.01 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7CKV Resolution: 1.75→45.489 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.477 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.123
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.374 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→45.489 Å
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Refine LS restraints |
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LS refinement shell |
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