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Yorodumi- PDB-6eky: Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eky | ||||||
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Title | Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with 1-naphthol (II) | ||||||
Components | Aromatic peroxygenaseUnspecific peroxygenase | ||||||
Keywords | OXIDOREDUCTASE / directed evolution / PaDaI / unspecific peroxygenase / UPO / heme-thiolate peroxidase / Agrocybe aegerita / 1-naphthol / 1-Naphthalenol | ||||||
Function / homology | Function and homology information unspecific peroxygenase / hydrogen peroxide catabolic process / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Agrocybe aegerita (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.23 Å | ||||||
Authors | Ramirez-Escudero, M. / Sanz-Aparicio, J. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eky.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eky.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 6eky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6eky ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6eky | HTTPS FTP |
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-Related structure data
Related structure data | 5oxtC 5oxuSC 5oy1C 5oy2C 6ekwC 6ekxC 6ekzC 6el0C 6el4C S: Starting model for refinement C: citing same article (ref.) |
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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 / Sugars , 2 types, 6 molecules A
#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.) Agrocybe aegerita (fungus) / Gene: APO1 / Plasmid: pPiczalphaB / Production host: Komagataella phaffii CBS 7435 (fungus) / Strain (production host): X-33 / References: UniProt: B9W4V6, unspecific peroxygenase |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 8 types, 415 molecules
#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-1NP / #9: Chemical | ChemComp-MOH / #10: 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: 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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
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: 1.23→48.06 Å / Num. obs: 96881 / % possible obs: 99.7 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.23→1.25 Å |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5OXU Resolution: 1.23→48.06 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.562 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / 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: 15.524 Å2
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Refinement step | Cycle: 1 / Resolution: 1.23→48.06 Å
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Refine LS restraints |
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