+Open data
-Basic information
Entry | Database: PDB / ID: 7qf5 | ||||||
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Title | Structure of the Q103L mutant of miniSOG | ||||||
Components | miniSOG (Q103L 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: 1.37 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 | 7qf5.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qf5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qf5_validation.pdf.gz | 814.6 KB | Display | wwPDB validaton report |
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Full document | 7qf5_full_validation.pdf.gz | 815.6 KB | Display | |
Data in XML | 7qf5_validation.xml.gz | 9 KB | Display | |
Data in CIF | 7qf5_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/7qf5 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/7qf5 | HTTPS FTP |
-Related structure data
Related structure data | 7qf2C 7qf3C 7qf4C 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: 14869.806 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, 165 molecules
#2: Chemical | ChemComp-FMN / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-CO / |
#5: Chemical | ChemComp-MG / |
#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: 2.06 Å3/Da / Density % sol: 40.4 % |
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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: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2015 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→38.38 Å / Num. obs: 23979 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 1 / Rrim(I) all: 0.06 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.37→1.41 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1734 / CC1/2: 0.643 / Rrim(I) all: 1.07 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GPU Resolution: 1.37→38.379 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.075 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.057 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: 17.635 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→38.379 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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