Better models by discarding data?

Background: CBMs are, generally, functionally and structurally autonomous from their associated catalytic domains. Results: The structure of a novel cellulase, BhCel5B, reveals that the appended carbohydrate-binding module, CBM46, extends the enzyme catalytic cleft. Conclusion: CBM46 targets BhCel5B to xyloglucan and is part of the catalytic cleft required for the hydrolysis of ␤-1,3-1,4-glucans. Significance: CBM46 has a dual role in the hydrolysis of complex carbohydrates by BhCel5B.

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“…c CC1 ⁄ 2 is the half-data set correlation coefficient (51). d Values for the outer shell are given in parentheses.…”

Section: Resultsmentioning

confidence: 99%

Family 46 Carbohydrate-binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and β-1,3–1,4-Glucans through Distinct Mechanisms

Venditto¹,

Najmudin²,

Luís

et al. 2015

Journal of Biological Chemistry

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“…Values in parentheses are for the highest resolution shell; the data were truncated at I/ (I) > 1.0 (Diederichs & Karplus, 2013 Supplementary Table S1; data-merging statistics are presented in Supplementary Fig. S2 and Supplementary Table S4.…”

Section: Acta Cryst (2017) D73 738-748mentioning

confidence: 99%

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

Clabbers

Genderen

Wan

et al. 2017

Acta Crystallogr D Struct Biol

100

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Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 mm 3 , i.e. no more than 6 Â 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 Â 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

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“…Further structure refinement and analysis for both crystalline forms are ongoing. 2.1 (36.5) 8.0 (3.5/30.4) † CC 1/2 is the half data-set correlation coefficient (Diederichs & Karplus, 2013). ‡ R merge = P hkl P i jI i ðhklÞ À hIðhklÞij= P hkl jF obs j, where I i (hkl) is the ith intensity measurement of reflection hkl, including symmetry-related reflections, and hI(hkl)i is its average.…”

Section: Data Collection and Processing Of Ctgh43 Crystalsmentioning

confidence: 99%

Crystallization and preliminary X-ray crystallographic analysis of a novel α-L-arabinofuranosidase (CtGH43) fromClostridium thermocellumATCC 27405

et al. 2014

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The truncated carbohydrate-active enzyme belonging to family 43 glycoside hydrolase from Clostridium thermocellum (CtGH43) is an -l-arabinofuranosidase that in combination with endoxylanase leads to complete breakdown of l-arabinosyl-substituted xylans. The recombinant enzyme CtGH43 from C. thermocellum was overexpressed in Escherichia coli and purified by immobilized metal-ion affinity chromatography. The recombinant CtGH43 has a molecular mass of 35.86 kDa. Preliminary structural characterization was carried out on CtGH43 crystallized from different conditions, which gave either cube-shaped or brick-shaped crystals. These diffracted to a resolution of 1.65 Å for the cubic form and 1.1 Å for the monoclinic form. Molecular replacement was used to solve the CtGH43 structure.

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Better models by discarding data?

Cited by 218 publications

References 16 publications

Family 46 Carbohydrate-binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and β-1,3–1,4-Glucans through Distinct Mechanisms

Family 46 Carbohydrate-binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and β-1,3–1,4-Glucans through Distinct Mechanisms

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

Crystallization and preliminary X-ray crystallographic analysis of a novel α-L-arabinofuranosidase (CtGH43) fromClostridium thermocellumATCC 27405

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