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- PDB-6ekx: Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ekx | ||||||
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Title | Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with 1-naphthol (I) | ||||||
![]() | Aromatic peroxygenase | ||||||
![]() | OXIDOREDUCTASE / directed evolution / PaDaI / unspecific peroxygenase / UPO / heme-thiolate peroxidase / Agrocybe aegerita / 1-naphthol / 1-Naphthalenol | ||||||
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 | ![]() | 98.1 KB | Display | ![]() |
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PDB format | ![]() | 71.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 957.7 KB | Display | ![]() |
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Full document | ![]() | 963.5 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oxtC ![]() 5oxuSC ![]() 5oy1C ![]() 5oy2C ![]() 6ekwC ![]() 6ekyC ![]() 6ekzC ![]() 6el0C ![]() 6el4C 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 8 types, 470 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/1NP.gif)
![](data/chem/img/MOH.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/1NP.gif)
![](data/chem/img/MOH.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 | #8: Chemical | #9: Chemical | ChemComp-MOH / #10: 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: 1.6M sodium potassium phosphate pH 5.6, 3% MPD, soaking 100mM 1-Naphthol, 20% methanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2015 / Details: KB mirrors |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→48.04 Å / Num. obs: 124527 / % possible obs: 99 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.13→1.14 Å / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2 / Num. unique obs: 5458 / Rpim(I) all: 0.369 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OXU Resolution: 1.13→48.04 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.454 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033 / 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: 12.996 Å2
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Refinement step | Cycle: 1 / Resolution: 1.13→48.04 Å
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Refine LS restraints |
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