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Yorodumi- PDB-4au9: Crystal Structure of a Fungal DyP-Type Peroxidase from Auriculari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4au9 | |||||||||
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Title | Crystal Structure of a Fungal DyP-Type Peroxidase from Auricularia auricula-judae | |||||||||
Components | DYP-TYPE PEROXIDASE IDye decolorizing peroxidase | |||||||||
Keywords | OXIDOREDUCTASE / HEME / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information dye decolorizing peroxidase / lactoperoxidase activity / peroxidase / peroxidase activity / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | AURICULARIA AURICULA-JUDAE (ear fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Strittmatter, E. / Pecyna, M. / Ullrich, R. / Hofrichter, M. / Plattner, D.A. / Liers, C. / Piontek, K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: First Crystal Structure of a Fungal High-Redox Potential Dye-Decolorizing Peroxidase: Substrate Interaction Sites and Long-Range Electron Transfer. Authors: Strittmatter, E. / Liers, C. / Ullrich, R. / Wachter, S. / Hofrichter, M. / Plattner, D.A. / Piontek, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4au9.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4au9.ent.gz | 157.5 KB | Display | PDB format |
PDBx/mmJSON format | 4au9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/4au9 ftp://data.pdbj.org/pub/pdb/validation_reports/au/4au9 | HTTPS FTP |
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-Related structure data
Related structure data | 2d3qS S: Starting model for refinement |
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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: (-0.34081, 0.92871, -0.14607), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46987.066 Da / Num. of mol.: 2 / Fragment: DYP-TYPE PEROXIDASE DOMAIN, RESIDUES 1-448 / Source method: isolated from a natural source Details: GERMAN COLLECTION OF MICROORGANISMS (DSM), ACCESS NUMBER DSMZ 11326 Source: (natural) AURICULARIA AURICULA-JUDAE (ear fungus) / Strain: SXM9-C021 References: UniProt: I2DBY1*PLUS, dye decolorizing peroxidase |
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-Sugars , 3 types, 5 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar |
-Non-polymers , 5 types, 689 molecules
#4: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-ACT / | #8: Chemical | ChemComp-TAM / | #9: Water | ChemComp-HOH / | |
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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: 2.15 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.17 M SODIUM ACETATE TRIHYDRATE 0.085 M TRIS HYDROCHLORIDE PH 8.5 25.5% POLYETHYLENE GLYCOL 4000 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.01 Å / Num. obs: 49651 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.02 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.35 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D3Q Resolution: 2.1→49.03 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.889 / SU B: 3.451 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→49.03 Å
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Refine LS restraints |
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