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Open data
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Basic information
Entry | Database: PDB / ID: 1b82 | ||||||
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Title | PRISTINE RECOMB. LIGNIN PEROXIDASE H8 | ||||||
![]() | PROTEIN (LIGNIN PEROXIDASE) | ||||||
![]() | OXIDOREDUCTASE / LIGNIN DEGRADATION / HEME / RADICAL REACTION / ELECTRON TRANSFER | ||||||
Function / homology | ![]() lignin peroxidase / diarylpropane peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blodig, W. / Doyle, W.A. / Smith, A.T. / Piontek, K. | ||||||
![]() | ![]() Title: Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications ...Title: Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism. Authors: Blodig, W. / Smith, A.T. / Doyle, W.A. / Piontek, K. #1: Journal: Biochemistry / Year: 1998 Title: Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis. Authors: Doyle, W.A. / Blodig, W. / Veitch, N.C. / Piontek, K. / Smith, A.T. #2: Journal: Biochemistry / Year: 1998 Title: Autocatalytic formation of a hydroxy group at C beta of trp171 in lignin peroxidase. Authors: Blodig, W. / Doyle, W.A. / Smith, A.T. / Winterhalter, K. / Choinowski, T. / Piontek, K. #3: Journal: Biochem.J. / Year: 1996 Title: Expression of lignin peroxidase H8 in Escherichia coli: folding and activation of the recombinant enzyme with Ca2+ and haem. Authors: Doyle, W.A. / Smith, 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 | ![]() | 158.7 KB | Display | ![]() |
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PDB format | ![]() | 122.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 47.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b80SC ![]() 1b85C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.258, -0.966, -0.008), Vector: |
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Components
#1: Protein | Mass: 37480.719 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE Source method: isolated from a genetically manipulated source Details: HEME CONTAINING / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||
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Crystal grow | pH: 3.5 / Details: pH 3.5 | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 69484 / % possible obs: 94.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 4.3 / % possible all: 89.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 234766 |
Reflection shell | *PLUS % possible obs: 89.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1B80 Resolution: 1.8→30 Å / SU B: 2.16 / Cross valid method: THROUGHOUT / σ(F): 0 Details: ANISOTROPIC SCALING (REFMAC) WAS USED TO ACCOUNT FOR CRYSTAL ANISOTROPICITY PRISTINE LIGNIN PEROXIDASE HAS NOT REACTED WITH PEROXIDES. CRYSTALLISATION AND DATA COLLECTION WERE DONE IN THE ...Details: ANISOTROPIC SCALING (REFMAC) WAS USED TO ACCOUNT FOR CRYSTAL ANISOTROPICITY PRISTINE LIGNIN PEROXIDASE HAS NOT REACTED WITH PEROXIDES. CRYSTALLISATION AND DATA COLLECTION WERE DONE IN THE PRESENCE OF THE PHENOLIC ANTIOXIDANT ORCINOL.
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Displacement parameters | Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.163 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.254 / Rfactor obs: 0.189 |