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- PDB-4fdq: The crystal structures of several mutants of pleurotus eryngii ve... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fdq | ||||||
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Title | The crystal structures of several mutants of pleurotus eryngii versatile peroxidase | ||||||
![]() | Versatile peroxidase VPL2 | ||||||
![]() | OXIDOREDUCTASE / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / AROMATIC-SUBSTRATE BINDING | ||||||
Function / homology | ![]() versatile peroxidase / reactive-black-5:hydrogen-peroxide oxidoreductase activity / manganese peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mate, M.J. / Romero, A. / Ruiz-Duenas, F.J. / Martinez, A.T. | ||||||
![]() | ![]() Title: Two Oxidation Sites for Low Redox Potential Substrates: A DIRECTED MUTAGENESIS, KINETIC, AND CRYSTALLOGRAPHIC STUDY ON PLEUROTUS ERYNGII VERSATILE PEROXIDASE. Authors: Morales, M. / Mate, M.J. / Romero, A. / Martinez, M.J. / Martinez, A.T. / Ruiz-Duenas, F.J. #1: ![]() Title: Site-directed mutagenesis of the catalytic tryptophan environment in Pleurotus eryngii versatile peroxidase. Authors: Ruiz-Duenas, F.J. / Morales, M. / Mate, M.J. / Romero, A. / Martinez, M.J. / Smith, A.T. / 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 | ![]() | 85.4 KB | Display | ![]() |
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PDB format | ![]() | 61.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 827.4 KB | Display | ![]() |
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Full document | ![]() | 833.1 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fcnC ![]() 4fcsC ![]() 4fefC ![]() 4g05C ![]() 2vkaS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33146.113 Da / Num. of mol.: 1 / Fragment: UNP residues 31-349 / Mutation: E140G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 392 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.4 M ammonium sulfate, 0.1 M sodium cacodilate and 2% 1,3-propanediol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 20, 2007 |
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.12 Å / Num. all: 59138 / Num. obs: 57998 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 13.182 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.2 / Num. unique all: 8340 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VKA Resolution: 1.6→48.12 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.107 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.064 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.316 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→48.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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