+Open data
-Basic information
Entry | Database: PDB / ID: 6y4j | ||||||
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Title | Engineered Fructosyl Peptide Oxidase | ||||||
Components | Fructosyl Peptide Oxidase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Donini, S. / Rigoldi, F. / Gautieri, A. / Parisini, E. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Biotechnol.Bioeng. / Year: 2020 Title: Rational backbone redesign of a fructosyl peptide oxidase to widen its active site access tunnel. Authors: Rigoldi, F. / Donini, S. / Torretta, A. / Carbone, A. / Redaelli, A. / Bandiera, T. / 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 | 6y4j.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y4j.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 6y4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/6y4j ftp://data.pdbj.org/pub/pdb/validation_reports/y4/6y4j | HTTPS FTP |
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-Related structure data
Related structure data | 5t1eS S: Starting model for refinement |
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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
#1: Protein | Mass: 48179.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star | ||||
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#2: Chemical | ChemComp-FAD / | ||||
#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: 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: 2.81 Å3/Da / Density % sol: 56.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES monohydrate pH 6.5, 12% PEG 20 K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→45.8 Å / Num. obs: 118634 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.014 / Rrim(I) all: 0.073 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.35→1.42 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 9.9 / Num. unique obs: 17077 / CC1/2: 0.986 / Rpim(I) all: 0.083 / Rrim(I) all: 0.415 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T1E Resolution: 1.38→45.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.608 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.047 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.05 Å2 / Biso mean: 15.52 Å2 / Biso min: 5.39 Å2
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Refinement step | Cycle: final / Resolution: 1.38→45.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.38→1.416 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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