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Yorodumi- PDB-4w7j: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICUL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w7j | ||||||
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Title | CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE | ||||||
Components | Dye-decolorizing peroxidase | ||||||
Keywords | OXIDOREDUCTASE / DECOLORIZING PEROXIDASE (DYP) / 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: 1.79 Å | ||||||
Authors | Medrano, F.J. / Romero, A. | ||||||
Citation | 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 | 4w7j.cif.gz | 359.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w7j.ent.gz | 291.4 KB | Display | PDB format |
PDBx/mmJSON format | 4w7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/4w7j ftp://data.pdbj.org/pub/pdb/validation_reports/w7/4w7j | HTTPS FTP |
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-Related structure data
Related structure data | 4w7kC 4w7lC 4w7mC 4w7nC 4w7oC 4afvS 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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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47107.305 Da / Num. of mol.: 4 / Fragment: UNP residues 62-509 / Mutation: yes 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 #2: Chemical | ChemComp-HEM / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 32.5% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 150630 / % possible obs: 97.1 % / Redundancy: 4.1 % / Net I/σ(I): 6.59 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 1.03 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AFV Resolution: 1.79→39.356 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.86 / 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: 1.79→39.356 Å
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Refine LS restraints |
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LS refinement shell |
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