+Open data
-Basic information
Entry | Database: PDB / ID: 4uzi | ||||||||||||
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Title | Crystal Structure of AauDyP Complexed with Imidazole | ||||||||||||
Components | DYE-DECOLORIZING PEROXIDASE | ||||||||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / DYP-TYPE PEROXIDASE / 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. / Liers, C. / Ullrich, R. / Hofrichter, M. / Piontek, K. / Plattner, D.A. | ||||||||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2015 Title: The Toolbox of Auricularia Auricula-Judae Dye-Decolorizing Peroxidase - Identification of Three New Potential Substrate-Interaction Sites. Authors: Strittmatter, E. / Serrer, K. / Liers, C. / Ullrich, R. / Hofrichter, M. / Piontek, K. / Schleicher, E. / Plattner, D.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uzi.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uzi.ent.gz | 158.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/4uzi ftp://data.pdbj.org/pub/pdb/validation_reports/uz/4uzi | HTTPS FTP |
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-Related structure data
Related structure data | 4au9S 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46805.855 Da / Num. of mol.: 2 / Fragment: DYP-TYPE PEROXIDASE DOMAIN, RESIDUES 64-509 / 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, dye decolorizing peroxidase |
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-Sugars , 3 types, 6 molecules
#2: 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 |
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#3: 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 |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 11 types, 559 molecules
#4: Chemical | #6: Chemical | ChemComp-IMD / #7: Chemical | ChemComp-MRD / ( | #8: Chemical | ChemComp-MPD / ( #9: Chemical | ChemComp-FMT / | #10: Chemical | #11: Chemical | ChemComp-ACT / #12: Chemical | ChemComp-OXD / | #13: Chemical | #14: Chemical | ChemComp-GOA / | #15: Water | ChemComp-HOH / | |
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-Details
Sequence details | PRECURSOR SEQUENCE IN GENBANK AFJ79723.1 WITH PROLONGED N-TERMINUS. |
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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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 30% MPD, 10% PEG 4000, 100 MM IMIDAZOLE-HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.954 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.5 Å / Num. obs: 50456 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.31 |
Reflection shell | Resolution: 2.1→2.22 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.72 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AU9 Resolution: 2.1→47.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.382 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY PROBABLY BOTH ENANTIOMERS OF MPD OCCUPY THE BINDING SITE OF MPD36D IN VARIOUS CONFORMATIONS. IN LIGHT OF THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY PROBABLY BOTH ENANTIOMERS OF MPD OCCUPY THE BINDING SITE OF MPD36D IN VARIOUS CONFORMATIONS. IN LIGHT OF THE 2.1 A RESOLUTION, ONLY ONE REPRESENTATIVE (S ENANTIOMER) WAS DEEMED MEANINGFUL.
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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: 22.348 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→47.51 Å
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