+Open data
-Basic information
Entry | Database: PDB / ID: 1b85 | ||||||
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Title | LIGNIN PEROXIDASE | ||||||
Components | Ligninase H8 | ||||||
Keywords | OXIDOREDUCTASE / LIGNIN DEGRADATION / HEME / RADICAL REACTION / ELECTRON TRANSFER / Calcium / Cleavage on pair of basic residues / Disulfide bond / Glycoprotein / Hydrogen peroxide / Iron / Metal-binding / Peroxidase / Zymogen | ||||||
Function / homology | Function and homology information 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 | Phanerochaete chrysosporium (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Blodig, W. / Doyle, W.A. / Smith, A.T. / Piontek, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 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: 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b85.cif.gz | 161.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b85.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 1b85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b85_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1b85_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1b85_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 1b85_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b85 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b85 | HTTPS FTP |
-Related structure data
Related structure data | 1b80SC 1b82C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.24991, -0.96826, 0.005), Vector: |
-Components
#1: Protein | Mass: 37441.684 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE / Mutation: W171F SUBSTITUTION Source method: isolated from a genetically manipulated source Details: HEME CONTAINING / Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: BKM 1767 / Gene: LIP H8, LPOA / Plasmid: PFLAG1-LIPP / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P06181, lignin peroxidase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | ALA 114, PROBABLY SEQUENCING | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||
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Crystal grow | pH: 4 / Details: pH 4.0 | ||||||||||||||||||||
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: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→12 Å / Num. obs: 62663 / % possible obs: 91.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.4 / % possible all: 89.6 |
Reflection | *PLUS Lowest resolution: 12 Å / Num. measured all: 392354 |
Reflection shell | *PLUS % possible obs: 89.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B80 Resolution: 1.85→12 Å / SU B: 2.17 / Cross valid method: THROUGHOUT / σ(F): 0 Details: ANISOTROPIC SCALING (REFMAC) WAS USED TO ACCOUNT FOR CRYSTAL ANISOTROPICITY
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Displacement parameters | Biso mean: 21.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→12 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.142 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.23 / Rfactor obs: 0.164 |