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- PDB-6el4: Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6el4 | ||||||
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Title | Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with veratryl alcohol | ||||||
![]() | Aromatic peroxygenase | ||||||
![]() | OXIDOREDUCTASE / directed evolution / PaDaI / unspecific peroxygenase / UPO / heme-thiolate peroxidase / Agrocybe aegerita / veratryl alcohol / 3 / 4-Dimethoxybenzyl alcohol | ||||||
Function / homology | ![]() unspecific peroxygenase / hydrogen peroxide catabolic process / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramirez-Escudero, M. / Sanz-Aparicio, J. | ||||||
![]() | ![]() Title: Structural Insights into the Substrate Promiscuity of a Laboratory-Evolved Peroxygenase. Authors: Ramirez-Escudero, M. / Molina-Espeja, P. / Gomez de Santos, P. / Hofrichter, M. / Sanz-Aparicio, J. / Alcalde, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.7 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 921.1 KB | Display | ![]() |
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Full document | ![]() | 925.7 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oxtC ![]() 5oxuSC ![]() 5oy1C ![]() 5oy2C ![]() 6ekwC ![]() 6ekxC ![]() 6ekyC ![]() 6ekzC ![]() 6el0C S: Starting model for refinement C: citing same article ( |
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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
-Protein / Sugars , 2 types, 6 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 35947.934 Da / Num. of mol.: 1 / Mutation: V57A, L67F, V75I, I248V, F311L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 364 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/VOH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/VOH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ChemComp-CL / | ||||
#6: Chemical | ChemComp-PO4 / | ||||
#7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-VOH / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.15 % / Description: Cluster of plates |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.6 M sodium potassium phosphate pH 5.6, soaking 50mM veratryl alcohol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2014 / Details: KB mirror |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→48.04 Å / Num. obs: 50107 / % possible obs: 99.2 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.042 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2432 / CC1/2: 0.869 / Rpim(I) all: 0.277 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OXU Resolution: 1.53→48.04 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.051 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.067 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.315 Å2
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Refinement step | Cycle: 1 / Resolution: 1.53→48.04 Å
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Refine LS restraints |
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