[English] 日本語
Yorodumi- PDB-3fmu: Crystal Structure Analysis of Fungal Versatile Peroxidase from Pl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fmu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii | ||||||
Components | Versatile peroxidase VPL2 | ||||||
Keywords | 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 / Heme / Hydrogen peroxide / Iron / Manganese / Metal-binding / Secreted / Zymogen | ||||||
Function / homology | Function and homology information 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 | Pleurotus eryngii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||
Authors | Piontek, K. / Martinez, A.T. / Choinowski, T. / Plattner, D.A. | ||||||
Citation | Journal: To be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fmu.cif.gz | 211.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fmu.ent.gz | 169.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/3fmu ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fmu | HTTPS FTP |
---|
-Related structure data
Related structure data | 3fjwC 3fkgSC 3fm1C 3fm4C 3fm6C C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34506.570 Da / Num. of mol.: 1 / Mutation: W164S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pleurotus eryngii (fungus) / Strain: IJFM, A169 / Gene: VPL2 / Plasmid: PFLAG1-VPL2 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 / References: UniProt: O94753, versatile peroxidase |
---|
-Non-polymers , 6 types, 541 molecules
#2: Chemical | ChemComp-HEM / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-FE / #6: Chemical | ChemComp-CAC / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.17 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 14% PEG 8000, 100mM Zn-acetate, 100mM Na-cacodylate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.891976 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2003 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.891976 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→80 Å / Num. all: 191427 / Num. obs: 186809 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.98 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.097 / Net I/σ(I): 11.95 |
Reflection shell | Resolution: 1.03→1.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 4.57 / Num. unique all: 53827 / Rsym value: 0.254 / % possible all: 91.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FKG Resolution: 1.04→44.688 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.349 / SU ML: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 12.107 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→44.688 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.04→1.067 Å / Total num. of bins used: 20
|