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Yorodumi- PDB-5ag1: DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ag1 | |||||||||
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Title | DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) with meso- nitrated heme | |||||||||
Components | DYE-DECOLORIZING PEROXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / DYP / FUNGAL / HEME / GLYCOPROTEIN / NITRATION | |||||||||
Function / homology | Function and homology information dye decolorizing peroxidase / lactoperoxidase activity / peroxidase / peroxidase activity / heme binding / extracellular region / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | AURICULARIA AURICULA-JUDAE (ear fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Strittmatter, E. / Piontek, K. / Plattner, D.A. | |||||||||
Citation | Journal: To be Published Title: Crystallographic Trapping of a Covalently Modified Heme in a Dye-Decolorizing Peroxidase Authors: Strittmatter, E. / Piontek, K. / 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 | 5ag1.cif.gz | 202.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ag1.ent.gz | 161 KB | Display | PDB format |
PDBx/mmJSON format | 5ag1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5ag1 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5ag1 | HTTPS FTP |
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-Related structure data
Related structure data | 5ag0C 4au9S C: citing same article (ref.) 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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-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 DSM 11326 Source: (natural) AURICULARIA AURICULA-JUDAE (ear fungus) / Strain: SXM9-C021 / References: UniProt: I2DBY1, dye decolorizing peroxidase |
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-Sugars , 2 types, 5 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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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 908 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | ChemComp-FMT / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | DELTA-MESO NITROHEME (N7H): IRON PROTOPORPHSequence details | PRECURSOR SEQUENCE IN GENBANK 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.17 M SODIUM ACETATE TRIHYDRATE, 0.085 M SODIUM CACODYLATE PH 6.5, 25% (W/V) PEG 8000, 15% (V/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→44.57 Å / Num. obs: 75411 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.11 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AU9 Resolution: 1.85→44.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.131 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY PROTEIN WAS TREATED WITH PROLI NONOATE AND PERACETIC ACID PRIOR TO CRYSTALLIZATION.
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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: 16.212 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→44.57 Å
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Refine LS restraints |
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