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Yorodumi- PDB-7pn5: Evolved unspecific peroxygenase with A77L mutation in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pn5 | ||||||
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Title | Evolved unspecific peroxygenase with A77L mutation in complex with hexane | ||||||
Components | Aromatic peroxygenase | ||||||
Keywords | OXIDOREDUCTASE / Hexane 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: 1.82 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 | 7pn5.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pn5.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 7pn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/7pn5 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/7pn5 | HTTPS FTP |
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-Related structure data
Related structure data | 7pn4C 7pn6C 7pn7C 7pn8C 7pn9C 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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#7: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 259 molecules
#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
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-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: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.5M sodium potassium phosphate pH 5.6, 3% MPD Soaking: 19.5% hexane, 36 hours, cryoprotected with 25% glycerol |
-Data collection
Diffraction | Mean temperature: 291 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: Jun 3, 2020 / Details: MIRRORS KB |
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: 1.82→44.93 Å / Num. obs: 30212 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.267 / Rpim(I) all: 0.12 / Rrim(I) all: 0.294 / Χ2: 0.78 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.82→1.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1767 / Rpim(I) all: 0.307 / Rrim(I) all: 0.773 / Χ2: 0.56 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5OXU Resolution: 1.82→44.97 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.861 / SU B: 3.873 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.16 / 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: 54.66 Å2 / Biso mean: 20.223 Å2 / Biso min: 12.43 Å2
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Refinement step | Cycle: final / Resolution: 1.82→44.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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