+Open data
-Basic information
Entry | Database: PDB / ID: 8bjy | ||||||
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Title | Engineered Fructosyl Peptide Oxidase - X02B mutant | ||||||
Components | Fructosyl Peptide Oxidase mutant (X02B) | ||||||
Keywords | OXIDOREDUCTASE / FAD / deglycating enzyme / Amadori product / Fructosyl Peptide Oxidase | ||||||
Function / homology | saccharopine oxidase activity / MTOX family / sarcosine oxidase activity / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily / flavin adenine dinucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / FAD dependent oxidoreductase domain-containing protein Function and homology information | ||||||
Biological species | Parastagonospora nodorum SN15 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.475 Å | ||||||
Authors | Estiri, H. / Bhattacharya, S. / Rodriguez-Buitrago, J.A. / Parisini, E. | ||||||
Funding support | 1items
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Citation | Journal: Sci Rep / Year: 2023 Title: Tailoring FPOX enzymes for enhanced stability and expanded substrate recognition. Authors: Estiri, H. / Bhattacharya, S. / Buitrago, J.A.R. / Castagna, R. / Legzdina, L. / Casucci, G. / Ricci, A. / Parisini, E. / Gautieri, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bjy.cif.gz | 190 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bjy.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/8bjy ftp://data.pdbj.org/pub/pdb/validation_reports/bj/8bjy | HTTPS FTP |
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-Related structure data
Related structure data | 8blxC 8blzC 8bmuC 6y4jS S: Starting model for refinement 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
#1: Protein | Mass: 48148.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parastagonospora nodorum SN15 (fungus) / Strain: SN15 / ATCC MYA-4574 / FGSC 10173 / Gene: SNOG_08398 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0UIL6 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #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: 2.64 Å3/Da / Density % sol: 53.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 20000 16-26%, MES 0.1M pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.475→63.421 Å / Num. obs: 82805 / % possible obs: 96 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.07 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.475→1.501 Å / Redundancy: 11.3 % / Num. unique obs: 4255 / Rrim(I) all: 0.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y4J Resolution: 1.475→63.421 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.187 / SU B: 1.806 / SU ML: 0.061 / Average fsc free: 0.9493 / Average fsc work: 0.9548 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.073 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: 26.915 Å2
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Refinement step | Cycle: LAST / Resolution: 1.475→63.421 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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