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Yorodumi- PDB-6ywr: Structure of Chloroflexus aggregans flavin based fluorescent prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ywr | ||||||
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Title | Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148H variant (space group C2) | ||||||
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
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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 | 6ywr.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ywr.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ywr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ywr_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ywr_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6ywr_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6ywr_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6ywr ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6ywr | HTTPS FTP |
-Related structure data
Related structure data | 6ywgC 6ywhC 6ywiC 6ywqC 6yxcC 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
#1: Protein | Mass: 12410.900 Da / Num. of mol.: 2 / Mutation: Q148H 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-SO4 / #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: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.5 M Lithium sulfate monohydrate, 15% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→54.87 Å / Num. obs: 35488 / % possible obs: 96.4 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.046 / Rrim(I) all: 0.085 / Net I/σ(I): 9.5 / Num. measured all: 114941 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6rhf Resolution: 1.5→54.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.43 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075 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: 65.55 Å2 / Biso mean: 16.478 Å2 / Biso min: 8.2 Å2
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Refinement step | Cycle: final / Resolution: 1.5→54.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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