catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding Similarity search - Function
: / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive ...: / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Beta Barrel / Mainly Beta Similarity search - Domain/homology
Journal: Proteins / Year: 2015 Title: Unprecedented access of phenolic substrates to the heme active site of a catalase: Substrate binding and peroxidase-like reactivity of Bacillus pumilus catalase monitored by X-ray ...Title: Unprecedented access of phenolic substrates to the heme active site of a catalase: Substrate binding and peroxidase-like reactivity of Bacillus pumilus catalase monitored by X-ray crystallography and EPR spectroscopy. Authors: Loewen, P.C. / Villanueva, J. / Switala, J. / Donald, L.J. / Ivancich, A.
Mass: 18.015 Da / Num. of mol.: 1495 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate pH 4.6, 50 mM NaCl, 10 mM CoCl2 and 12-20% 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→104.13 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2471 / WRfactor Rwork: 0.2155 / FOM work R set: 0.7319 / SU B: 10.312 / SU ML: 0.153 / SU R Cruickshank DPI: 0.2318 / SU Rfree: 0.1856 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2614
7647
5.2 %
RANDOM
Rwork
0.2297
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-
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obs
0.2314
147764
90.83 %
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all
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149181
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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
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