[English] 日本語
Yorodumi- PDB-2yp1: Crystallization of a 45 kDa peroxygenase- peroxidase from the mus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yp1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron | |||||||||
Components | AROMATIC PEROXYGENASEUnspecific peroxygenase | |||||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE/PEROXYGENASE / UNSPECIFIC/AROMATIC PEROXYGENASE / HEME / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information unspecific peroxygenase / peroxidase activity / hydrogen peroxide catabolic process / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | AGROCYBE AEGERITA (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Piontek, K. / Strittmatter, E. / Ullrich, R. / Plattner, D.A. / Hofrichter, M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yp1.cif.gz | 304.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yp1.ent.gz | 256 KB | Display | PDB format |
PDBx/mmJSON format | 2yp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2yp1 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2yp1 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-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) AGROCYBE AEGERITA (fungus) / Strain: TM-A1 / References: UniProt: B9W4V6, unspecific peroxygenase |
---|
-Sugars , 6 types, 20 molecules
#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 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#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
#7: Chemical | ChemComp-HEM / #8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-ACT / #10: Chemical | ChemComp-SO4 / #12: Water | ChemComp-HOH / | |
---|
-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 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46 % / Description: NONE |
---|---|
Crystal grow | pH: 4.6 Details: 2.0M AMMONIUM SULFATE, 200MM SODIUM ACETATE, PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 |
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: 0.976 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→48.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.465 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→48.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|