+Open data
-Basic information
Entry | Database: PDB / ID: 7qf2 | ||||||
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Title | Structure of miniSOG reconstituted with riboflavin as a cofactor | ||||||
Components | miniSOG | ||||||
Keywords | FLAVOPROTEIN / LOV DOMAIN / RIBOFLAVIN / PHOTOSENSITIZING PROTEIN / FLUORESCENT PROTEIN | ||||||
Function / homology | : / RIBOFLAVIN Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 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 | 7qf2.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qf2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qf2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7qf2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7qf2_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7qf2_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/7qf2 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/7qf2 | HTTPS FTP |
-Related structure data
Related structure data | 7qf3C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 14999.865 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, 157 molecules
#2: Chemical | ChemComp-RBF / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Chemical | ChemComp-CO / | #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: 39.9 % |
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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: ID23-1 / Wavelength: 0.973 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 23, 2014 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→38.25 Å / Num. obs: 91259 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.07→1.1 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.12 / Num. unique obs: 6739 / CC1/2: 0.563 / Rrim(I) all: 1.12 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GPU Resolution: 1.07→38.243 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.931 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.027 / ESU R Free: 0.028 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: 12.796 Å2
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Refinement step | Cycle: LAST / Resolution: 1.07→38.243 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 / % reflection obs: 100 %
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