Experimental charge density from electron microscopic maps

Wang, Jimin

doi:10.1002/pro.3198

Cited by 29 publications

(36 citation statements)

References 38 publications

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“…The effect of possible resolution underestimation in protein crystallography on the ED peak maximum for an atom of given B ‐factor can be numerically estimated using error‐free simulation (see Methods), that is the percentage contribution of the Fourier terms to the peak maximum beyond the maximal resolution S max that are omitted in calculation. The results obtained show that for any given percentage, the slope of ln [ S max ] versus ln [ B ] is approximately ½ for both this error‐free simulation and the experimental data because the product B [ S max ] term is dimensionless (Fig. ).…”

Section: Resultsmentioning

confidence: 83%

“…The results are then plotted in the form of S max versus B and in the natural logarithm form of ln [ S max ] versus ln [ B ], and are compared with the experimental data adopted from recent studies (Fig. ) . The results obtained here are independent of specific molecule used in this study, or specific atomic coordinates, or the upper limit of 0.2‐Å resolution used in the study.…”

Section: Methodsmentioning

confidence: 87%

“…Experimental CD maps were calculated from ESP maps as described previously . Structure factors for corresponding Fourier transforms were obtained using the programs CCP4 and Phenix, which were used for recalculation of maps in any non‐grid point through direct Fourier summation.…”

Section: Methodsmentioning

confidence: 99%

“…With sufficiently large B values, peaks for bonded atoms may be merged, resulting in unresolvable atomic shapes. A single logarithm–logarithm relationship exists in X‐ray crystallography between the lattice resolution of an experimental ED map and the Wilson B ‐factor of the diffraction data . This study presents a quantitative theory to describe how the peak maximum for an atom in an ED map varies as a function of atomic B value at sub‐Å resolution, and then extends it to structures at much lower resolution.…”

Section: Introductionmentioning

confidence: 92%

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Determination of chemical identity and occupancy from experimental density maps

Wang

2017

Protein Science

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Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity-based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B-factor in Fourier transforms of the corresponding maps. An application of this theory is described to an experimental ED map at 1.73-Å resolution, and to an experimental CD map at 2.2-Å resolution. All the three density functions are linearly proportional to occupancy when the structure factor F(000) term of Fourier transforms of experimental density maps is included. Upon application of this theory to both experimental CD and ESP maps recently reported for photosystem II-light harvesting complex II supercomplex at 3.2-Å resolution, the occupancy of two extrinsic protein subunits PsbQ and PsbP is determined to be 20.4 ± 0.2%, and the negative mean ESP value of vitreous ice displaced by the supercomplex on electron scattering path is estimated to be 3% of the mean ESP value of protein α-helices.

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Section: Resultsmentioning

confidence: 83%

Section: Methodsmentioning

confidence: 87%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 92%

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Determination of chemical identity and occupancy from experimental density maps

Wang

2017

Protein Science

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“…Particles from the two sessions were then pooled for the final round of 3D auto-refine. A charge density map was calculated in Chimera 40 as previously described 41 . Post-processing was also performed in RELION to generate a Fourier shell correlation (FSC) curve.…”

Section: Manuscript P a G E | 27 Of 32mentioning

confidence: 99%

Phazolicin – a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way

Travin

Watson

Metelev

et al. 2019

Preprint

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Y.S.P.). Travin D.Y. et al. Manuscript P a g e | 2 of 32 ABSTRACT Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly expanding and largely untapped class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display an outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium sp.Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ)an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants belonging to the Rhizobiales. PHZ inhibits prokaryotic translation through the obstruction of the passage of the nascent peptide through the ribosome exit channel. The cryo-EM structure of the Escherichia coli ribosome with bound PHZ revealed that the drug interacts with the 23S rRNA and ribosomal proteins uL4 and uL22 and obstructs the exit tunnel in a way that is distinct from other compounds blocking the exit channel. Weshow that the sequence of uL4 ribosomal protein loop involved in PHZ binding determines the species-specificity of antibiotic interaction with its target. PHZ and its predicted homologs from other bacterial species expand the known diversity of LAPs and may be used in the future as biocontrol agents for the needs of agriculture.

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On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets

et al. 2017

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In 2012, Karplus and Diederichs demonstrated that the Pearson correlation coefficient CC is a far better indicator of the quality and resolution of crystallographic data sets than more traditional measures like merging R-factor or signal-to-noise ratio. More specifically, they proposed that CC be computed for data sets in thin shells of increasing resolution so that the resolution dependence of that quantity can be examined. Recently, however, the CC values of entire data sets, i.e., cumulative correlation coefficients, have been used as a measure of data quality. Here, we show that the difference in cumulative CC value between a data set that has been accurately measured and a data set that has not is likely to be small. Furthermore, structures obtained by molecular replacement from poorly measured data sets are likely to suffer from extreme model bias.

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Experimental charge density from electron microscopic maps

Cited by 29 publications

References 38 publications

Determination of chemical identity and occupancy from experimental density maps

Determination of chemical identity and occupancy from experimental density maps

Phazolicin – a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way

On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets

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