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Yorodumi- PDB-5ikg: Asymmetric sulfoxidation by engineering the heme pocket of a dye-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ikg | ||||||
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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) / L357G 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 / molecular replacement / Resolution: 1.95 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: Linde, D. / 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 | 5ikg.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ikg.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ikg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5ikg ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5ikg | HTTPS FTP |
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-Related structure data
Related structure data | 5ikdC 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
#1: Protein | Mass: 46660.746 Da / Num. of mol.: 1 / Fragment: UNP residues 65-509 / Mutation: L357G 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: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 5% MPD (v/v), 100 mM MES (pH 6.5) and 15% PEG 6000 (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.95→44.73 Å / Num. obs: 35827 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Net I/σ(I): 12.6 / Num. measured all: 239457 / Scaling rejects: 19 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4W7J Resolution: 1.95→44.725 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.32 Å2 / Biso mean: 46.1644 Å2 / Biso min: 28.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→44.725 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: 13
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