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- PDB-4w7k: 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: 4w7k | |||||||||
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Title | CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S 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 | ![]() | 506.2 KB | Display | ![]() |
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PDB format | ![]() | 419.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 47.2 KB | Display | |
Data in CIF | ![]() | 76.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4w7jC ![]() 4w7lC ![]() 4w7mC ![]() 4w7nC ![]() 4w7oC ![]() 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 47031.207 Da / Num. of mol.: 2 / Fragment: UNP residues 62-509 / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dyp1 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.55 % |
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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: 1.00791 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. obs: 364516 / % possible obs: 82.6 % / Redundancy: 6 % / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.05→1.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1 / % possible all: 29.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AFV Resolution: 1.05→33.627 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.5 / 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: 1.05→33.627 Å
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Refine LS restraints |
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LS refinement shell |
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