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- PDB-5ag1: DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ag1 | |||||||||
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Title | DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) with meso- nitrated heme | |||||||||
![]() | DYE-DECOLORIZING PEROXIDASE | |||||||||
![]() | OXIDOREDUCTASE / DYP / FUNGAL / HEME / GLYCOPROTEIN / NITRATION | |||||||||
Function / homology | ![]() dye decolorizing peroxidase / lactoperoxidase activity / peroxidase / peroxidase activity / heme binding / extracellular region / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Strittmatter, E. / Piontek, K. / Plattner, D.A. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.4 KB | Display | ![]() |
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PDB format | ![]() | 161 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 43.8 KB | Display | |
Data in CIF | ![]() | 65.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ag0C ![]() 4au9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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) ![]() |
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-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#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 ![](data/chem/img/CAC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/N7H.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/N7H.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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