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Yorodumi- PDB-7pn9: Evolved unspecific peroxygenase with A77L mutation in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pn9 | ||||||
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Title | Evolved unspecific peroxygenase with A77L mutation in complex with lauric acid | ||||||
Components | Aromatic peroxygenaseUnspecific peroxygenase | ||||||
Keywords | OXIDOREDUCTASE / Lauric acid complex / peroxygenase / peroxidase | ||||||
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: 1.85 Å | ||||||
Authors | Fernandez-Garcia, A. / Sanz-Aparicio, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids. Authors: Gomez de Santos, P. / Gonzalez-Benjumea, A. / Fernandez-Garcia, A. / Aranda, C. / Wu, Y. / But, A. / Molina-Espeja, P. / Mate, D.M. / Gonzalez-Perez, D. / Zhang, W. / Kiebist, J. / ...Authors: Gomez de Santos, P. / Gonzalez-Benjumea, A. / Fernandez-Garcia, A. / Aranda, C. / Wu, Y. / But, A. / Molina-Espeja, P. / Mate, D.M. / Gonzalez-Perez, D. / Zhang, W. / Kiebist, J. / Scheibner, K. / Hofrichter, M. / Swiderek, K. / Moliner, V. / Sanz-Aparicio, J. / Hollmann, F. / Gutierrez, A. / Alcalde, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pn9.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pn9.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/7pn9 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/7pn9 | HTTPS FTP |
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-Related structure data
Related structure data | 7pn4C 7pn5C 7pn6C 7pn7C 7pn8C 7pnaC 5oxuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 5 molecules A
#1: Protein | Mass: 35990.012 Da / Num. of mol.: 1 / Mutation: V57A, L67F, V75I, A77L, I248V, F311L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrocybe aegerita (fungus) / Gene: APO1 / Production host: Komagataella phaffii CBS 7435 (fungus) / References: UniProt: B9W4V6, unspecific peroxygenase |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 240 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-DAO / |
#9: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.74 % |
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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: 50 mM lauric acid, 1h30, cryoprotected with 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2020 / Details: KB MIRRORS |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.2 Å / Num. obs: 27775 / % possible obs: 97.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.061 / Rrim(I) all: 0.139 / Χ2: 1.16 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1611 / Rpim(I) all: 0.266 / Rrim(I) all: 0.636 / Χ2: 1.38 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5OXU Resolution: 1.85→48.16 Å / Cor.coef. Fo:Fc: 0.844 / Cor.coef. Fo:Fc free: 0.831 / SU B: 5.601 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.95 Å2 / Biso mean: 16.416 Å2 / Biso min: 7.86 Å2
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Refinement step | Cycle: final / Resolution: 1.85→48.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.852→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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