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Yorodumi- PDB-6ekw: Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ekw | ||||||
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Title | Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with naphthalene | ||||||
Components | Aromatic peroxygenase | ||||||
Keywords | OXIDOREDUCTASE / directed evolution / PaDaI / unspecific peroxygenase / UPO / heme-thiolate peroxidase / Agrocybe aegerita / Naphthalene | ||||||
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: 1.43 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 | 6ekw.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ekw.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ekw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ekw_validation.pdf.gz | 877 KB | Display | wwPDB validaton report |
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Full document | 6ekw_full_validation.pdf.gz | 880.8 KB | Display | |
Data in XML | 6ekw_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6ekw_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6ekw ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6ekw | HTTPS FTP |
-Related structure data
Related structure data | 5oxtC 5oxuSC 5oy1C 5oy2C 6ekxC 6ekyC 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, 474 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ChemComp-CL / | ||||
#6: Chemical | ChemComp-PO4 / | ||||
#7: Chemical | ChemComp-NPY / | ||||
#8: Chemical | ChemComp-GOL / #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: 1.4M sodium potassium phosphate pH 5.6, 3% MPD, soaking 20mM naphthalene, 20% methanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2015 / Details: KB mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→48.26 Å / Num. obs: 61029 / % possible obs: 98.5 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.043 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2 / Num. unique obs: 2783 / CC1/2: 0.752 / Rpim(I) all: 0.349 / % possible all: 91 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5OXU Resolution: 1.43→48.26 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.927 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.062 / 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: 14.306 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→48.26 Å
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Refine LS restraints |
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