[English] 日本語
Yorodumi- PDB-4bln: CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bln | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM III | ||||||
Components | VERSATILE PEROXIDASE I | ||||||
Keywords | OXIDOREDUCTASE / CLASS II FUNGAL PEROXIDASES | ||||||
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 OSTREATUS (oyster mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.149 Å | ||||||
Authors | Medrano, F.J. / Romero, A. | ||||||
Citation | Journal: Biotechnol.Biofuels / Year: 2014 Title: Ligninolytic Peroxidase Genes in the Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic and Stability Properties, and Lignin-Degrading Ability. Authors: Fernandez-Fueyo, E. / Ruiz-Duenas, F.J. / Martinez, M.J. / Romero, A. / Hammel, K.E. / Medrano, F.J. / Martinez, A.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bln.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bln.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bln_validation.pdf.gz | 794.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bln_full_validation.pdf.gz | 796.7 KB | Display | |
Data in XML | 4bln_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 4bln_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/4bln ftp://data.pdbj.org/pub/pdb/validation_reports/bl/4bln | HTTPS FTP |
-Related structure data
Related structure data | 4blkC 4bllC 4blxC 4blyC 4blzC 4bm0C 4bm1C 4bm2C 4bm3C 4bm4C 3fmuS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34794.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLEUROTUS OSTREATUS (oyster mushroom) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): W3110 / References: UniProt: Q9UR19*PLUS, versatile peroxidase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % / Description: NONE |
---|---|
Crystal grow | Details: 20 % PEG 3350 & 0.2 M AMMONIUM CHLORIDE. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. obs: 120788 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Biso Wilson estimate: 11.06 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.15→1.22 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.1 / % possible all: 98.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FMU Resolution: 1.149→47.3 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 17.32 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.003 Å2 / ksol: 0.355 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.149→47.3 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|