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Yorodumi- PDB-7qf3: Structure of the R57Q mutant of miniSOG expressed in E. coli in r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qf3 | ||||||
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Title | Structure of the R57Q mutant of miniSOG expressed in E. coli in regular LB medium | ||||||
Components | miniSOG (R57Q mutant) | ||||||
Keywords | FLAVOPROTEIN / LOV DOMAIN / RIBOFLAVIN / PHOTOSENSITIZING PROTEIN / FLUORESCENT PROTEIN | ||||||
Function / homology | : / FLAVIN MONONUCLEOTIDE Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Lafaye, C. / Aumonier, S. / von Stetten, D. / Noirclerc-Savoye, N. / Gotthard, G. / Royant, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Photochem Photobiol Sci / Year: 2022 Title: Riboflavin-binding proteins for singlet oxygen production. Authors: Lafaye, C. / Aumonier, S. / Torra, J. / Signor, L. / von Stetten, D. / Noirclerc-Savoye, M. / Shu, X. / Ruiz-Gonzalez, R. / Gotthard, G. / Royant, A. / Nonell, S. #1: Journal: Sci Rep / Year: 2019 Title: Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein. Authors: Torra, J. / Lafaye, C. / Signor, L. / Aumonier, S. / Flors, C. / Shu, X. / Nonell, S. / Gotthard, G. / Royant, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qf3.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qf3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/7qf3 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/7qf3 | HTTPS FTP |
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-Related structure data
Related structure data | 7qf2C 7qf4C 7qf5C 6gpuS 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
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 14855.712 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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-Non-polymers , 5 types, 104 molecules
#2: Chemical | ChemComp-FMN / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CO / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.04 Å3/Da / Density % sol: 39.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris-Hcl pH 8.0, 20 mM MgCl2, 28% PEG 4000, 15 mM CoCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9322 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2014 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9322 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→38.28 Å / Num. obs: 45101 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 1 / Rrim(I) all: 0.084 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4488 / CC1/2: 0.596 / Rrim(I) all: 1.199 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GPU Resolution: 1.1→38.28 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.169 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.031 / ESU R Free: 0.032 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.784 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→38.28 Å
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Refine LS restraints |
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LS refinement shell |
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