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Yorodumi- PDB-6yxc: Structure of Chloroflexus aggregans flavin based fluorescent prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yxc | ||||||
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Title | Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148R variant | ||||||
Components | Multi-sensor hybrid histidine kinase | ||||||
Keywords | FLUORESCENT PROTEIN / LOV domain | ||||||
Function / homology | Function and homology information cellular hyperosmotic response / histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / plasma membrane Similarity search - Function | ||||||
Biological species | Chloroflexus aggregans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Remeeva, A. / Nazarenko, V. / Kovalev, K. / Gushchin, I. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Proteins / Year: 2021 Title: Insights into the mechanisms of light-oxygen-voltage domain color tuning from a set of high-resolution X-ray structures. Authors: Remeeva, A. / Nazarenko, V.V. / Kovalev, K. / Goncharov, I.M. / Yudenko, A. / Astashkin, R. / Gordeliy, V. / Gushchin, I. #1: Journal: Biorxiv / Year: 2021 Title: Insights into the mechanisms of LOV domain color tuning from a set of high-resolution X-ray structures Authors: Remeeva, A. / Nazarenko, V.V. / Kovalev, K. / Goncharov, I. / Yudenko, A. / Astashkin, R. / Gordeliy, V. / Gushchin, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yxc.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yxc.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 6yxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yxc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6yxc_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6yxc_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 6yxc_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/6yxc ftp://data.pdbj.org/pub/pdb/validation_reports/yx/6yxc | HTTPS FTP |
-Related structure data
Related structure data | 6ywgC 6ywhC 6ywiC 6ywqC 6ywrC 6rhfS 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: 12429.947 Da / Num. of mol.: 2 / Mutation: Q148R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aggregans (strain MD-66 / DSM 9485) (bacteria) Strain: MD-66 / DSM 9485 / Gene: Cagg_3753 / Production host: Escherichia coli (E. coli) / References: UniProt: B8GAY9 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.12M hexanediol, 0.12M butanol, 0.12M 1,2-propanediol, 0.12M propanol, 0.12M butanediol, 0.12M 1,3-propanediol, 0.1M MES, 0.1M Imid, pH 6.5, 20%PEG500, 10% PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.632→39.78 Å / Num. obs: 22625 / % possible obs: 71.7 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.632→1.76 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1131 / CC1/2: 0.746 / % possible all: 18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6rhf Resolution: 1.65→39.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.396 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.121 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 76.88 Å2 / Biso mean: 25.248 Å2 / Biso min: 6.44 Å2
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Refinement step | Cycle: final / Resolution: 1.65→39.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.691 Å / Rfactor Rfree error: 0
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