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Yorodumi- PDB-6ywi: Structure of Chloroflexus aggregans flavin based fluorescent prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ywi | ||||||
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Title | Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148E variant | ||||||
Components | Multi-sensor hybrid histidine kinase | ||||||
Keywords | FLUORESCENT PROTEIN / LOV domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chloroflexus aggregans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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 | 6ywi.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ywi.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ywi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6ywi ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6ywi | HTTPS FTP |
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-Related structure data
Related structure data | 6ywgC 6ywhC 6ywqC 6ywrC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12401.867 Da / Num. of mol.: 2 / Mutation: Q148E 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-MES / | #4: Chemical | #5: 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: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1M glutamic acid, 0.1M alanine, 0.1M glycine, 0.1M lysine, 0.1M serine, 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: 0.972 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.13→54.92 Å / Num. obs: 86013 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Net I/σ(I): 12.3 / Num. measured all: 540189 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
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: 1.13→48.18 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.49 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 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: 55.2 Å2 / Biso mean: 14.851 Å2 / Biso min: 8.83 Å2
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Refinement step | Cycle: final / Resolution: 1.13→48.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.13→1.159 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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