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Yorodumi- PDB-6uv8: Crystal structure of a far-red cyanobacteriochrome photoreceptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uv8 | ||||||
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Title | Crystal structure of a far-red cyanobacteriochrome photoreceptor at room temperature | ||||||
Components | Multi-sensor signal transduction histidine kinase | ||||||
Keywords | SIGNALING PROTEIN / Photoreceptor / bilin-binding protein / far-red light | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Anabaena cylindrica | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å | ||||||
Authors | Yang, X. / Ren, Z. / Bandara, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Crystal structure of a far-red-sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism. Authors: Bandara, S. / Rockwell, N.C. / Zeng, X. / Ren, Z. / Wang, C. / Shin, H. / Martin, S.S. / Moreno, M.V. / Lagarias, J.C. / Yang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uv8.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uv8.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 6uv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/6uv8 ftp://data.pdbj.org/pub/pdb/validation_reports/uv/6uv8 | HTTPS FTP |
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-Related structure data
Related structure data | 6uvbC 4glqS C: citing same article (ref.) S: Starting model for refinement |
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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: 22056.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena cylindrica (strain ATCC 27899 / PCC 7122) (bacteria) Strain: ATCC 27899 / PCC 7122 / Gene: Anacy_2551 / Production host: Escherichia coli (E. coli) / References: UniProt: K9ZI18 |
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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: 4.56 Å3/Da / Density % sol: 73 % |
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Crystal grow | Temperature: 297 K / Method: batch mode / pH: 5.5 Details: 2 mg/mL protein, 8.5-10.5% polyethylene glycol 10,000 (PEG), 50 mM NH4CH3COO, and 50 mM Bis-tris buffer at pH 5.5 |
-Data collection
Diffraction | Mean temperature: 297 K / Ambient temp details: room temperature / Serial crystal experiment: Y | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.98-1.2 | |||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 12, 2018 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. obs: 8453 / % possible obs: 98.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 66.58 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 43.4 | |||||||||
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 397 / % possible all: 99.8 | |||||||||
Serial crystallography sample delivery | Description: crystal-on-crystal device / Method: fixed target | |||||||||
Serial crystallography sample delivery fixed target | Description: crystal-on-crystal device / Motion control: inSituX | |||||||||
Serial crystallography data reduction | Frames total: 800 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GLQ Resolution: 2.701→48.657 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 7 / Phase error: 23.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 264.14 Å2 / Biso mean: 99.4901 Å2 / Biso min: 37.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.701→48.657 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 20.5307 Å / Origin y: 45.9984 Å / Origin z: 19.8407 Å
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Refinement TLS group | Selection details: chain A |