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- PDB-4bll: Crystal Structure of Fungal Versatile Peroxidase I from Pleurotus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bll | ||||||
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Title | Crystal Structure of Fungal Versatile Peroxidase I from Pleurotus ostreatus - Crystal Form II | ||||||
![]() | VERSATILE PEROXIDASE I | ||||||
![]() | OXIDOREDUCTASE / CLASS II FUNGAL PEROXIDASES | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Medrano, F.J. / Romero, A. | ||||||
![]() | ![]() Title: Ligninolytic Peroxidase Genes in the Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic and Stability Properties, and Lignin-Degrading Ability. Authors: Fernandez-Fueyo, E. / Ruiz-Duenas, F.J. / Martinez, M.J. / Romero, A. / Hammel, K.E. / Medrano, 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 | ![]() | 188.9 KB | Display | ![]() |
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PDB format | ![]() | 151.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802 KB | Display | ![]() |
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Full document | ![]() | 804.4 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4blkC ![]() 4blnC ![]() 4blxC ![]() 4blyC ![]() 4blzC ![]() 4bm0C ![]() 4bm1C ![]() 4bm2C ![]() 4bm3C ![]() 4bm4C ![]() 3fmuS 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
#1: Protein | Mass: 34794.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.26 % / Description: NONE |
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Crystal grow | Details: 0.1 M NA-ACETATE AT PH 4.5 & 20 % PEG-1000, 0.2 M ZN(OAC)2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Date: Nov 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 154452 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Biso Wilson estimate: 9.33 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.1→1.17 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.6 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3FMU Resolution: 1.099→44.477 Å / SU ML: 0.08 / σ(F): 1.42 / Phase error: 11.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.099→44.477 Å
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Refine LS restraints |
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LS refinement shell |
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