+Open data
-Basic information
Entry | Database: PDB / ID: 2igk | ||||||
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Title | Crystal structure of recombinant pyranose 2-oxidase | ||||||
Components | Pyranose oxidase | ||||||
Keywords | OXIDOREDUCTASE / GMC OXIDOREDUCTASE / ROSSMANN FOLD / PHBH FOLD / HOMOTETRAMER / 8-ALPHA-(N3) HISTIDYL FLAVINYLATION | ||||||
Function / homology | Function and homology information pyranose oxidase / pyranose oxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / flavin adenine dinucleotide binding / periplasmic space Similarity search - Function | ||||||
Biological species | Trametes ochracea (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Divne, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural basis for substrate binding and regioselective oxidation of monosaccharides at c3 by pyranose 2-oxidase. Authors: Kujawa, M. / Ebner, H. / Leitner, C. / Hallberg, B.M. / Prongjit, M. / Sucharitakul, J. / Ludwig, R. / Rudsander, U. / Peterbauer, C. / Chaiyen, P. / Haltrich, D. / Divne, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2igk.cif.gz | 960.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2igk.ent.gz | 812.5 KB | Display | PDB format |
PDBx/mmJSON format | 2igk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/2igk ftp://data.pdbj.org/pub/pdb/validation_reports/ig/2igk | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 69413.789 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes ochracea (fungus) / Gene: p2o / Plasmid: pET21 d(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q7ZA32, pyranose oxidase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-MES / #4: Water | ChemComp-HOH / | |
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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: 2.56 Å3/Da / Density % sol: 51.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 12-13% monomethyl ether PEG 2000, 0.1 M mes, 50 mM CaCl2, 25% glycerol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.095 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 22, 2004 |
Radiation | Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.095 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.2 Å / Num. all: 608237 / Num. obs: 517862 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.076 / Net I/σ(I): 12.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→39.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.589 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.106 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→39.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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