Ultratight crystal packing of a 10 kDa protein

Trillo-Muyo, Sergio; Jasilionis, Andrius; Domagalski, Marcin J.; Chruszcz, M.; Minor, Władek; Kuisienė, Nomeda; Arolas, Joan L.; Solà, Marı́a; Gomis‐Rüth, F. Xavier

doi:10.1107/s0907444912050135

Cited by 9 publications

(8 citation statements)

References 46 publications

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“…S2. Ultra-tight structures with solvent contents below the closedsphere packing limit (26%) have been reported in lowsymmetry as well as in high-symmetry space groups (Trillo-Muyo et al, 2013), essentially reflecting the expected empirical space-group frequency distribution (Wukovitz & Yeates, 1995;Kantardjieff & Rupp, 2003;Chruszcz et al, 2008). We see no justification to include a linear regression model of the categorical relationship between symmetry and solvent content in the MP predictions.…”

Section: Empirically Discovered Dependenciesmentioning

confidence: 72%

“…A plausible explanation for the small but significant increase in mean solvent content in the post-1970s analyses may be the now widespread availability of PCR-based molecular-biology techniques which enable heterologous overexpression of crystallizable variants of more intricate and rare proteins compared with the earlier, more stable and abundant proteins which almost exclusively had to be isolated from natural sources. Some of the few structures exceeding the closed-sphere packing limit of 26% solvent content have been analysed (Trillo-Muyo et al, 2013). The structures of dehydrated monoclinic lysozyme (Nagendra et al, 1998) may serve as examples of extremely compact structures with a solvent content as low as 9%.…”

Section: The Matthews Coefficientmentioning

confidence: 99%

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Ten years of probabilistic estimates of biocrystal solvent content: new insightsvianonparametric kernel density estimate

Weichenberger

Rupp

2014

Acta Cryst D Biol Crystallogr

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The probabilistic estimate of the solvent content (Matthews probability) was first introduced in 2003. Given that the Matthews probability is based on prior information, revisiting the empirical foundation of this widely used solvent-content estimate is appropriate. The parameter set for the original Matthews probability distribution function employed in MATTPROB has been updated after ten years of rapid PDB growth. A new nonparametric kernel density estimator has been implemented to calculate the Matthews probabilities directly from empirical solvent-content data, thus avoiding the need to revise the multiple parameters of the original binned empirical fit function. The influence and dependency of other possible parameters determining the solvent content of protein crystals have been examined. Detailed analysis showed that resolution is the primary and dominating model parameter correlated with solvent content. Modifications of protein specific density for low molecular weight have no practical effect, and there is no correlation with oligomerization state. A weak, and in practice irrelevant, dependency on symmetry and molecular weight is present, but cannot be satisfactorily explained by simple linear or categorical models. The Bayesian argument that the observed resolution represents only a lower limit for the true diffraction potential of the crystal is maintained. The new kernel density estimator is implemented as the primary option in the MATTPROB web application at http://www.ruppweb.org/mattprob/.

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Section: Empirically Discovered Dependenciesmentioning

confidence: 72%

Section: The Matthews Coefficientmentioning

confidence: 99%

Ten years of probabilistic estimates of biocrystal solvent content: new insightsvianonparametric kernel density estimate

Weichenberger

Rupp

2014

Acta Cryst D Biol Crystallogr

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“…The structure of the 10-kDa C-terminal domain of a putative U32 protease from Geobacillus thermoleovorans has been solved. This C-terminal domain shows a compact distorted open ␤-barrel made up of eight ␤-strands and may function in protein binding based on structure similarity analysis (83). If this is true, it can be concluded that the N-terminal domain of U32 proteases should function as a catalytic domain (Fig.…”

Section: Bacterial Collagenolytic Proteases From the U32 Familymentioning

confidence: 99%

Diversity, Structures, and Collagen-Degrading Mechanisms of Bacterial Collagenolytic Proteases

Zhang¹,

Ran²,

Li³

et al. 2015

Appl Environ Microbiol

104

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Bacterial collagenolytic proteases are important because of their essential role in global collagen degradation and because of their virulence in some human bacterial infections. Bacterial collagenolytic proteases include some metalloproteases of the M9 family from Clostridium or Vibrio strains, some serine proteases distributed in the S1, S8, and S53 families, and members of the U32 family. In recent years, there has been remarkable progress in discovering new bacterial collagenolytic proteases and in investigating the collagen-degrading mechanisms of bacterial collagenolytic proteases. This review provides comprehensive insight into bacterial collagenolytic proteases, especially focusing on the structures and collagen-degrading mechanisms of representative bacterial collagenolytic proteases in each family. The roles of bacterial collagenolytic proteases in human diseases and global nitrogen cycling, together with the biotechnological and medical applications for these proteases, are also briefly discussed.

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“…of only 20% is among the lowest known for protein crystals (30). Although these features are consistent with the extraordinary stability of OBs, these structures are incomplete, with over 30 of the 245 amino acids undefined by electron density.…”

Section: Significancementioning

confidence: 60%

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

Gati

Oberthüer

Yefanov

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm 3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm 3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.XFEL | nanocrystals | structural biology | bioimaging | SFX I maging of biomolecules using radiation of short enough wavelength to resolve individual atoms is limited by radiation damage, which destroys the very structure being measured. Energy absorption is unavoidable because the ratio of elastic scattering to damaging photoabsorption is an inherent property of atoms. Absorbed dose is therefore proportional to the scattered intensity, and thus the measured signal, used to determine the structure. The maximum tolerable dose that the sample can withstand fundamentally limits atomic resolution structure determination (1). The tolerable dose, and therefore damage, is a function of spatial resolution, with fine detail being destroyed first (2, 3). Radiation damage is typically overcome by distributing the dose over many identical copies of the same molecule, either using crystals containing many aligned copies of the same molecule, or by aligning images of individual molecules in the case of single particle electron microscopy. At room temperature, free radical production after a dose as small as 150 kGy (gray = J _ kg −1 absorbed energy) causes rapid decay of biological samples (4). This decay can be reduced by cooling the sample to below ∼120 K....

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Ultratight crystal packing of a 10 kDa protein

Cited by 9 publications

References 46 publications

Ten years of probabilistic estimates of biocrystal solvent content: new insightsvianonparametric kernel density estimate

Ten years of probabilistic estimates of biocrystal solvent content: new insightsvianonparametric kernel density estimate

Diversity, Structures, and Collagen-Degrading Mechanisms of Bacterial Collagenolytic Proteases

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

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