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- PDB-7o2d: Unspecific peroxygenase from Hypoxylon sp. EC38 in complex with 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o2d | ||||||
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Title | Unspecific peroxygenase from Hypoxylon sp. EC38 in complex with 2-(N-morpholino) ethanesulfonic acid (MES) | ||||||
![]() | Peroxygenase | ||||||
![]() | OXIDOREDUCTASE / peroxygenase / heme | ||||||
Function / homology | Chloroperoxidase / Chloroperoxidase-like superfamily / Peroxidase, family 2 / Heme haloperoxidase family profile. / peroxidase activity / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Cloroperoxidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rotilio, L. / Mattevi, A. | ||||||
![]() | ![]() Title: Structural and biochemical studies enlighten the unspecific peroxygenase from Hypoxylon sp. EC38 as an efficient oxidative biocatalyst. Authors: Rotilio, L. / Swoboda, A. / Ebner, K. / Rinnofner, C. / Glieder, A. / Kroutil, W. / Mattevi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.4 KB | Display | ![]() |
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PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 389.1 KB | Display | ![]() |
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Full document | ![]() | 390.8 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 9.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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, 3 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 28461.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Sugar |
-Non-polymers , 4 types, 7 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MES / |
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#4: Chemical | ChemComp-HEM / |
#5: Chemical | ChemComp-MG / |
#6: 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: 3.62 Å3/Da / Density % sol: 66.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG500 MME, 10% PEG20000, 0.1 M MES monohydrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.68→29.81 Å / Num. obs: 12383 / % possible obs: 99.8 % / Redundancy: 26.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.027 / Rrim(I) all: 0.139 / Net I/σ(I): 22.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() 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: 161.4 Å2 / Biso mean: 56.255 Å2 / Biso min: 37.12 Å2
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Refinement step | Cycle: final / Resolution: 2.68→29.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.682→2.751 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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