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Yorodumi- PDB-8k9o: Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k9o | ||||||||||||
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Title | Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state | ||||||||||||
Components | histidine kinase | ||||||||||||
Keywords | SIGNALING PROTEIN / Cyanobacteriochrome / chromatic acclimation | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Microchaete diplosiphon (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||||||||
Authors | Nagae, T. / Hirose, Y. / Mishima, M. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Sci Adv / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k9o.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k9o.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 8k9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/8k9o ftp://data.pdbj.org/pub/pdb/validation_reports/k9/8k9o | 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 & homologyF&H Search |
-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: 22045.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microchaete diplosiphon (bacteria) / Gene: rcaE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47897, histidine kinase |
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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: 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: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.1211 Å |
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: 1.1211 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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