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- PDB-7pn4: Evolved unspecific peroxygenase with A77L mutation in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pn4 | ||||||
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Title | Evolved unspecific peroxygenase with A77L mutation in complex with naphthalene | ||||||
![]() | Aromatic peroxygenase | ||||||
![]() | OXIDOREDUCTASE / Naphthalene complex / peroxygenase / peroxidase | ||||||
Function / homology | ![]() unspecific peroxygenase / hydrogen peroxide catabolic process / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fernandez-Garcia, A. / Sanz-Aparicio, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.2 KB | Display | ![]() |
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PDB format | ![]() | 62.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pn5C ![]() 7pn6C ![]() 7pn7C ![]() 7pn8C ![]() 7pn9C ![]() 7pnaC ![]() 5oxuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#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.) ![]() ![]() |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 8 types, 177 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NPY.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NPY.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/GOL.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-NPY / | ||||
#7: Chemical | ChemComp-PO4 / | ||||
#8: Chemical | #9: Chemical | ChemComp-GOL / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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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, 5% MPD Soaking: 30 mM naphthalene, 2 hours, cryoprotected with 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 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: 2.05→48.1 Å / Num. obs: 20970 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.071 / Rrim(I) all: 0.185 / Χ2: 0.96 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1622 / Rpim(I) all: 0.281 / Rrim(I) all: 0.726 / Χ2: 1.06 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OXU Resolution: 2.05→48.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.347 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.166 / 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: 93.3 Å2 / Biso mean: 24.626 Å2 / Biso min: 14.39 Å2
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Refinement step | Cycle: final / Resolution: 2.05→48.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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