[English] 日本語
Yorodumi- PDB-4w7l: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICUL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w7l | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. D168N MUTANT | ||||||
Components | Dye-decolorizing peroxidase | ||||||
Keywords | OXIDOREDUCTASE / HEME / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information dye decolorizing peroxidase / lactoperoxidase activity / peroxidase / peroxidase activity / heme binding / extracellular region / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Auricularia auricula-judae (ear fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4w7l.cif.gz | 516.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4w7l.ent.gz | 426.4 KB | Display | PDB format |
PDBx/mmJSON format | 4w7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/4w7l ftp://data.pdbj.org/pub/pdb/validation_reports/w7/4w7l | HTTPS FTP |
---|
-Related structure data
Related structure data | 4w7jC 4w7kC 4w7mC 4w7nC 4w7oC 4afvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47106.316 Da / Num. of mol.: 2 / 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 | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.68 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00791 Å |
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: 405267 / % possible obs: 91.5 % / Redundancy: 5.8 % / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.05→1.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.7 / % possible all: 54.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AFV Resolution: 1.05→37.714 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.61 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→37.714 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|