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Yorodumi- PDB-5ikd: Asymmetric sulfoxidation by engineering the heme pocket of a dye-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ikd | ||||||||||||
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Title | Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase | ||||||||||||
Components | Dye-decolorizing peroxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / DECOLORIZING PEROXIDASE (DYP) / F359G VARIANT / HEME | ||||||||||||
Function / homology | Function and homology information dye decolorizing peroxidase / lactoperoxidase activity / peroxidase / peroxidase activity / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Auricularia auricula-judae (ear fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.109 Å | ||||||||||||
Authors | Romero, A. / Davo-Siguero, I. / Martinez, A.T. | ||||||||||||
Funding support | Spain, 1items
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Citation | Journal: Catalysis Science And Technology / Year: 2016 Title: Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase Authors: Linde, D. / Canellas, M. / Davo-Siguero, I. / Romero, A. / Lucas, F. / Ruiz-Duenas, F.J. / Guallar, V. / Martinez, A.T. #1: Journal: Biochem. J. / Year: 2015 Title: Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study. Authors: Pogni, R. / Canellas, M. / Lucas, F. / Guallar, V. / Baratto, M.C. / Sinicropi, A. / Saez-Jimenez, V. / Coscolin, C. / Romero, A. / Medrano, F.J. / Ruiz-Duenas, F.J. / Martinez, A.T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ikd.cif.gz | 260.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ikd.ent.gz | 210.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ikd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5ikd ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5ikd | HTTPS FTP |
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-Related structure data
Related structure data | 5ikgC 4w7jS 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
#1: Protein | Mass: 46713.805 Da / Num. of mol.: 1 / Fragment: UNP residues 64-509 / Mutation: F359G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Auricularia auricula-judae (ear fungus) Gene: dyp1 / Production host: Escherichia coli (E. coli) / References: UniProt: I2DBY1, dye decolorizing peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 2M magnesium formate and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.109→46.63 Å / Num. obs: 184770 / % possible obs: 98.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 9.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.5 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4W7J Resolution: 1.109→41.261 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.87 Å2 / Biso mean: 14.0754 Å2 / Biso min: 5.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.109→41.261 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: 14
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