+Open data
-Basic information
Entry | Database: PDB / ID: 7aby | ||||||||||||
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Title | Crystal structure of iLOV-Q489K mutant | ||||||||||||
Components | Phototropin-2 | ||||||||||||
Keywords | SIGNALING PROTEIN / LOV domain / BLUE LIGHT PHOTORECEPTOR / FLAVOPROTEIN | ||||||||||||
Function / homology | Function and homology information chloroplast relocation / negative regulation of anion channel activity by blue light / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity ...chloroplast relocation / negative regulation of anion channel activity by blue light / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||||||||
Authors | Granzin, J. / Batra-Safferling, R. | ||||||||||||
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: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aby.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aby.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 7aby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/7aby ftp://data.pdbj.org/pub/pdb/validation_reports/ab/7aby | HTTPS FTP |
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-Related structure data
Related structure data | 6yx4C 6yx6C 6yxbC 7ab6C 7ab7C 4eesS 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: 15045.925 Da / Num. of mol.: 1 / Mutation: D491(SNN), G492(ACY), Q489K Source method: isolated from a genetically manipulated source Details: modified residues: Asp491-Gly492 to SNN L-3-AMINOSUCCINIMIDE and ACY ACETIC ACID including the required backbone bonds. Asp-Gly form a Succinimide intermediate. Keyword: Deamidation Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT2, CAV1, KIN7, NPL1, At5g58140, K21L19.6 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P93025, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-ACT / |
#4: 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: 1.82 Å3/Da / Density % sol: 32.56 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, 25 % (w/v) PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9194 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9194 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→43.93 Å / Num. obs: 20710 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 19.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.025 / Rrim(I) all: 0.074 / Net I/σ(I): 14.3 / Num. measured all: 186700 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.482
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EES Resolution: 1.45→38.937 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.3 Å2 / Biso mean: 24.9037 Å2 / Biso min: 12.97 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→38.937 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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