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- PDB-4w7o: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICUL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4w7o | ||||||
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Title | CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. G169L, Y147S AND W377S TRIPLE MUTANT | ||||||
![]() | Dye-decolorizing peroxidase | ||||||
![]() | OXIDOREDUCTASE / DECOLORIZING PEROXIDASE (DYP) / HEME | ||||||
Function / homology | ![]() dye decolorizing peroxidase / lactoperoxidase activity / peroxidase / peroxidase activity / heme binding / extracellular region / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Medrano, F.J. / Romero, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.5 KB | Display | ![]() |
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PDB format | ![]() | 212.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.4 KB | Display | ![]() |
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Full document | ![]() | 790 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 39.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4w7jC ![]() 4w7kC ![]() 4w7lC ![]() 4w7mC ![]() 4w7nC ![]() 4afvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46988.184 Da / Num. of mol.: 1 / Fragment: UNP residues 62-509 / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dyp1 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005822 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 147432 / % possible obs: 99.2 % / Redundancy: 6.4 % / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.2→1.27 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 3.1 / % possible all: 45.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AFV Resolution: 1.2→46.305 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.79 / 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: 1.2→46.305 Å
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Refine LS restraints |
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LS refinement shell |
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