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- PDB-3fm1: 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: 3fm1 | ||||||
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Title | Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii | ||||||
![]() | Versatile peroxidase VPL2 | ||||||
![]() | OXIDOREDUCTASE / 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 / Calcium / Heme / Hydrogen peroxide / Iron / Manganese / Metal-binding / Organic radical / 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 | ![]() | 101.7 KB | Display | ![]() |
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PDB format | ![]() | 74.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 821.8 KB | Display | ![]() |
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Full document | ![]() | 825.4 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fjwC ![]() 3fkgSC ![]() 3fm4C ![]() 3fm6C ![]() 3fmuC 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: 34676.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 767 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-MN / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | |
-Details
Sequence details | THERE IS A CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THIS CAN BE ...THERE IS A CONFLICT 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: 2.91 Å3/Da / Density % sol: 57.71 % |
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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; Crystals were soaked with Mn2+; VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→25 Å / Num. all: 40092 / Num. obs: 40092 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 9.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.74→1.78 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 2671 / Rsym value: 0.297 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3FKG Resolution: 1.78→24.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.187 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.095 / 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: 19.591 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→24.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.826 Å / Total num. of bins used: 20
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