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Yorodumi- PDB-5oc3: Crystal structure of Ser67Cys/Pro121Cys Amadoriase I mutant from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oc3 | ||||||
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Title | Crystal structure of Ser67Cys/Pro121Cys Amadoriase I mutant from Aspergillus Fumigatus | ||||||
Components | Fructosyl amine:oxygen oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / thermoresistance / flavin dependant enzyme / glycated aminoacid | ||||||
Function / homology | Function and homology information fructosyl-amino acid oxidase activity / saccharopine oxidase activity / sarcosine oxidase activity / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å | ||||||
Authors | Rigoldi, F. / Donini, S. / Gautieri, A. / Parisini, E. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: Thermal stabilization of the deglycating enzyme Amadoriase I by rational design. Authors: Rigoldi, F. / Donini, S. / Giacomina, F. / Sorana, F. / 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 | 5oc3.cif.gz | 213.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oc3.ent.gz | 166.2 KB | Display | PDB format |
PDBx/mmJSON format | 5oc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/5oc3 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/5oc3 | HTTPS FTP |
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-Related structure data
Related structure data | 5oc2C 4wctS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51358.844 Da / Num. of mol.: 2 / Mutation: S67C/P121C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (mold) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O42629, UniProt: Q4WIF5*PLUS #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate pH 5.6 14% PEG4K 15 % isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1529→47.886 Å / Num. obs: 56549 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.95 |
Reflection shell | Resolution: 2.1529→2.27 Å / Redundancy: 7 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 8145 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4wct Resolution: 2.153→47.886 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.153→47.886 Å
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Refine LS restraints |
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LS refinement shell |
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