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- PDB-3fkg: Crystal Structure Analysis of Fungal Versatile Peroxidase from Pl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fkg | ||||||
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Title | Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii | ||||||
![]() | Versatile peroxidase VPL2 | ||||||
![]() | OXIDOREDUCTASE / ALLELIC VARIANT / AROMATIC-SUBSTRATE BINDING / CLASS II (FUNGAL)PEROXIDASES / protoporphyrin IX / ELECTRON TRANSFER / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / MN-INDEPENDENT OXIDATION PHENOLIC NON-PHENOLIC AROMATICS / MNII OXIDATION / PEROXIDASE / POLYVALENT PEROXIDASE / Heme / Hydrogen peroxide / Iron / Manganese / Metal-binding / Secreted / Zymogen | ||||||
Function / homology | ![]() versatile peroxidase / reactive-black-5:hydrogen-peroxide oxidoreductase activity / manganese peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Piontek, K. / Martinez, A.T. / Choinowski, T. / Plattner, D.A. | ||||||
![]() | ![]() Title: Structural and Site-directed Mutagenesis Study of Versatile Peroxidase Oxidizing both Mn(II) and Aromatic Substrates Authors: Piontek, K. / Choinowski, T. / Perez-Boada, M. / Ruiz-Duenas, F.J. / Martinez, M.J. / Plattner, D.A. / Martinez, A.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.8 KB | Display | ![]() |
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PDB format | ![]() | 65.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 847.9 KB | Display | ![]() |
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Full document | ![]() | 852.1 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fjwC ![]() 3fm1C ![]() 3fm4C ![]() 3fm6C ![]() 3fmuC ![]() 1qpaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34663.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 365 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THIS CAN BE ...THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THIS CAN BE CALLED AS SPONTANEIT |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 17% PEG 10000, 200mM Zn-acetate, 100mM Na-cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8065 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→40 Å / Num. all: 34670 / Num. obs: 33318 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.056 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.81→1.84 Å / Mean I/σ(I) obs: 1.1 / Rsym value: 0.392 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QPA Resolution: 1.81→32.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.617 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.889 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→32.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.857 Å / Total num. of bins used: 20
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