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- PDB-2yp1: Crystallization of a 45 kDa peroxygenase- peroxidase from the mus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yp1 | |||||||||
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Title | Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron | |||||||||
![]() | AROMATIC PEROXYGENASE![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Piontek, K. / Strittmatter, E. / Ullrich, R. / Plattner, D.A. / Hofrichter, M. | |||||||||
![]() | ![]() Title: Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits Authors: Piontek, K. / Strittmatter, E. / Ullrich, R. / Grobe, G. / Pecyna, M.J. / Kluge, M. / Scheibner, K. / Hofrichter, M. / Plattner, D.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization of a 45 kDa Peroxygenase/Peroxidase from the Mushroom Agrocybe Aegerita and Structure Determination by Sad Utilizing Only the Haem Iron. Authors: Piontek, K. / Ullrich, R. / Liers, C. / Diederichs, K. / Plattner, D.A. / Hofrichter, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.3 KB | Display | ![]() |
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PDB format | ![]() | 256 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | ![]() Mass: 35692.707 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: GERMAN COLLECTION OF MICROORGANISMS (DSM), ACCESS NUMBER DSMZ 22459 Source: (natural) ![]() ![]() ![]() |
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-Sugars , 6 types, 20 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 | ![]() Source method: isolated from a genetically manipulated source #4: 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: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #6: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #11: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 5 types, 1211 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-HEM / ![]() #8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-ACT / ![]() #10: Chemical | ChemComp-SO4 / ![]() #12: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | THE MATURE PROTEIN BEGINS AT E44 WITH RESPECT TO B9W4V6. CRYSTALLIZED PROTEIN BEGINS AT L47, THAT ...THE MATURE PROTEIN BEGINS AT E44 WITH RESPECT TO B9W4V6. CRYSTALLIZ |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow![]() | pH: 4.6 Details: 2.0M AMMONIUM SULFATE, 200MM SODIUM ACETATE, PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.31→48.9 Å / Num. obs: 97006 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.31→2.37 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.5 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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: 29.918 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→48.91 Å
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Refine LS restraints |
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