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Yorodumi- PDB-8q5f: Crystal structure of miniSOG protein from Arabidopsis thaliana wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q5f | ||||||
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Title | Crystal structure of miniSOG protein from Arabidopsis thaliana with covalent FMN | ||||||
Components | miniSOG | ||||||
Keywords | SIGNALING PROTEIN / covalent flavinylation | ||||||
Function / homology | FLAVIN MONONUCLEOTIDE Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Rozeboom, H.J. / Fraaije, M.W. | ||||||
Funding support | 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Fixing Flavins: Hijacking a Flavin Transferase for Equipping Flavoproteins with a Covalent Flavin Cofactor. Authors: Tong, Y. / Kaya, S.G. / Russo, S. / Rozeboom, H.J. / Wijma, H.J. / Fraaije, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q5f.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q5f.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 8q5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/8q5f ftp://data.pdbj.org/pub/pdb/validation_reports/q5/8q5f | HTTPS FTP |
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-Related structure data
Related structure data | 8q5eC 8q5gC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 13168.835 Da / Num. of mol.: 2 / Mutation: A51D T52I V53V Q54A K55G I56A R57T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli BL21 (bacteria) #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 19% polyacrylic acid 5100, 100 mM Hepes ppH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96456 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96456 Å / Relative weight: 1 |
Reflection | Resolution: 2→67.43 Å / Num. obs: 17411 / % possible obs: 91.8 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.036 / Rrim(I) all: 0.078 / Χ2: 1.04 / Net I/σ(I): 11.9 / Num. measured all: 69790 |
Reflection shell | Resolution: 2→2.05 Å / % possible obs: 98.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.98 / Num. measured all: 5601 / Num. unique obs: 1375 / CC1/2: 0.697 / Rpim(I) all: 0.514 / Rrim(I) all: 1.114 / Χ2: 1.01 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.961 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.602 Å2
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Refinement step | Cycle: 1 / Resolution: 2→56.65 Å
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Refine LS restraints |
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