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Yorodumi- PDB-4g05: The crystal structures of several mutants of Pleurotus eryngii ve... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g05 | ||||||
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Title | The crystal structures of several mutants of Pleurotus eryngii versatile peroxidase | ||||||
Components | Versatile peroxidase VPL2 | ||||||
Keywords | OXIDOREDUCTASE / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / AROMATIC-SUBSTRATE BINDING | ||||||
Function / homology | Function and homology information 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 | Pleurotus eryngii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Mate, M.J. / Romero, A. / Ruiz-Duenas, F.J. / Martinez, A.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 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: Journal: Biochemistry / Year: 2008 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. / 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 | 4g05.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g05.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 4g05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/4g05 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/4g05 | HTTPS FTP |
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-Related structure data
Related structure data | 4fcnC 4fcsC 4fdqC 4fefC 2vkaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33318.293 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-347 / Mutation: E140G, G191E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pleurotus eryngii (fungus) / Gene: vpl2 / Production host: Escherichia coli (E. coli) / References: UniProt: O94753, versatile peroxidase |
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-Non-polymers , 5 types, 172 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-JZ3 / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.31 % |
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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 CACODYLATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 21, 2008 |
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: 2.35→69 Å / Num. all: 18866 / Num. obs: 18856 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 15.55 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2762 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VKA Resolution: 2.35→69 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 4.934 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.459 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.405 Å / Total num. of bins used: 20
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