[English] 日本語
Yorodumi- PDB-6yxb: Structure of Chloroflexus aggregans flavin based fluorescent prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yxb | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21) | ||||||
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: 1.5 Å | ||||||
Authors | Remeeva, A. / Nazarenko, V. / Kovalev, K. / Gushchin, I. | ||||||
Funding support | Russian Federation, 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins. Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / ...Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / Jaeger, K.E. / Batra-Safferling, R. / Gushchin, I. / Krauss, U. #1: 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. #2: 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. #3: Journal: Biorxiv / Year: 2021 Title: Structural and mechanistic insight into spectral tuning in flavin-binding fluorescent proteins Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / ...Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / Jaeger, K.E. / Batra-Safferling, R. / Gushchin, I. / Krauss, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6yxb.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6yxb.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 6yxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yxb_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6yxb_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6yxb_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 6yxb_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/6yxb ftp://data.pdbj.org/pub/pdb/validation_reports/yx/6yxb | HTTPS FTP |
-Related structure data
Related structure data | 6yx4SC 6yx6C 7ab6C 7ab7C 7abyC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12401.934 Da / Num. of mol.: 4 / Mutation: Q148K 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 | ChemComp-FMN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.41 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.5M Ammonium Sulfate, 0.1M tri-Sodium citrate, pH 6.5, 1M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9737 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→110.54 Å / Num. obs: 76240 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.049 / Rrim(I) all: 0.087 / Net I/σ(I): 10.6 / Num. measured all: 228792 / Scaling rejects: 300 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6yx4 Resolution: 1.5→56.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.353 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.51 Å2 / Biso mean: 12.813 Å2 / Biso min: 5.52 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→56.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|