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Yorodumi- PDB-5fnb: CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fnb | ||||||
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Title | CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII SEPTUPLE MUTANT E37K, H39R, V160A, T184M, Q202L, D213A & G330R | ||||||
Components | VERSATILE PEROXIDASE VPL2 | ||||||
Keywords | OXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / PROTOPORPHYRIN IX / ELECTRON T LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / INDEPENDENT OXIDATION PHENOLIC NON-PHENOLIC AROMATICS / MNII OXIDATION / PEROXIDASE / POLYVALENT PEROXIDASE / OXIDOREDUCTASE HYDROGEN PEROXIDE / IRON / MANGANESE / METAL-BINDING / SECRETED | ||||||
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: 1.792 Å | ||||||
Authors | Medrano, F.J. / Romero, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2016 Title: Unveiling the Basis of Alkaline Stability of an Evolved Versatile Peroxidase. Authors: Saez-Jimenez, V. / Acebes, S. / Garcia-Ruiz, E. / Romero, A. / Guallar, V. / Alcalde, M. / Medrano, F.J. / Martinez, A.T. / Ruiz-Duenas, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fnb.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fnb.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fnb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5fnb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5fnb_validation.xml.gz | 31 KB | Display | |
Data in CIF | 5fnb_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/5fnb ftp://data.pdbj.org/pub/pdb/validation_reports/fn/5fnb | HTTPS FTP |
-Related structure data
Related structure data | 5fneC 3fmuS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34668.016 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLEUROTUS ERYNGII (fungus) / Strain: IJFM, A169 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 References: UniProt: O94753, versatile peroxidase, peroxidase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.48 % / Description: NONE |
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Crystal grow | Details: 0.1 M TRIS-HCL (PH 7.8), 5 % PEG3350, 1.25 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 59335 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.41 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 12 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.7 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FMU Resolution: 1.792→49.015 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 23.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.792→49.015 Å
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Refine LS restraints |
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LS refinement shell |
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