A Low Resolution Electron-Density Map of Lipoyl Transsuccinylase, the Core of the  -Ketoglutarate Dehydrogenase Complex

1972 ◽  
Vol 36 (0) ◽  
pp. 199-203 ◽  
Author(s):  
D. J. DeRosier ◽  
R. M. Oliver
Keyword(s):  
Electron Density ◽  
Low Resolution ◽  
The Core ◽  
Resolution Electron ◽  
Density Map ◽  
Electron Density Map ◽  
Dehydrogenase Complex ◽  
Ketoglutarate Dehydrogenase

scholarly journals HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions

2014 ◽  
Vol 70 (8) ◽  
pp. 2069-2084 ◽  
Author(s):  
Georgy Derevyanko ◽  
Sergei Grudinin
Keyword(s):  
Electron Density ◽  
Cross Correlation ◽  
Three Dimensional ◽  
Hermite Functions ◽  
Low Resolution ◽  
Atomic Structures ◽  
Resolution Electron ◽  
Laplacian Filter ◽  
Density Map ◽  
Electron Density Map

HermiteFit, a novel algorithm for fitting a protein structure into a low-resolution electron-density map, is presented. The algorithm accelerates the rotation of the Fourier image of the electron density by using three-dimensional orthogonal Hermite functions. As part of the new method, an algorithm for the rotation of the density in the Hermite basis and an algorithm for the conversion of the expansion coefficients into the Fourier basis are presented.HermiteFitwas implemented using the cross-correlation or the Laplacian-filtered cross-correlation as the fitting criterion. It is demonstrated that in the Hermite basis the Laplacian filter has a particularly simple form. To assess the quality of density encoding in the Hermite basis, an analytical way of computing the crystallographicRfactor is presented. Finally, the algorithm is validated using two examples and its efficiency is compared with two widely used fitting methods,ADP_EMandcoloresfrom theSituspackage.HermiteFitwill be made available at http://nano-d.inrialpes.fr/software/HermiteFit or upon request from the authors.

A Comparison of Two Algorithms for Electron-Density Map Improvement by Introduction of Atomicity: Skeletonization, and Map Sorting Followed by Refinement

1998 ◽  
Vol 54 (1) ◽  
pp. 81-85 ◽  
Author(s):  
F. M. D. Vellieux
Keyword(s):  
Electron Density ◽  
Initial Density ◽  
Acta Cryst ◽  
Density Maps ◽  
Resolution Electron ◽  
Crystallographic Symmetry ◽  
Density Map ◽  
Ornithine Transcarbamoylase ◽  
Electron Density Map ◽  
Pseudo Atom

A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148–157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347–351]. Tests carried out using the 3.0 Å resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762–10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3° is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4° is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions.

Application of the maximum entropy method to electron density determination

1985 ◽  
Vol 18 (6) ◽  
pp. 442-445 ◽  
Author(s):  
W. Wei
Keyword(s):  
Maximum Entropy ◽  
Electron Density ◽  
Entropy Method ◽  
X Ray Diffraction ◽  
Resolution Electron ◽  
Density Map ◽  
Electron Density Map ◽  
Principle Of Maximum ◽  
Better Than

The principle of maximum entropy is adopted to derive a procedure for obtaining the electron density distribution in crystals from incomplete X-ray diffraction data. This method was applied to cementite and the result proved to be better than the conventional Fourier inversion in resolution as well as in the absence of ripples. The potential advantages of this method are: (1) the amount of subjective judgment imposed on unavailable data is significantly limited, and (2) the result of this method is consistent with the known information and maximally noncommittal with regard to the unknowns. It is shown that the method is especially well suited to the problem of the determination of a high-resolution electron density map from insufficient experimental data.

The 4.5 Å Resolution Structure of a Bacterial Serine Protease from Streptomyces Griseus

1974 ◽  
Vol 52 (3) ◽  
pp. 208-220 ◽  
Author(s):  
P. W. Codding ◽  
L. T. J. Delbaere ◽  
K. Hayakawa ◽  
W. L. B. Hutcheon ◽  
M. N. G. James ◽  
...  
Keyword(s):  
Electron Density ◽  
Streptomyces Griseus ◽  
Protein Mass ◽  
Isomorphous Replacement ◽  
Resolution Electron ◽  
Cell Dimensions ◽  
Metal Derivatives ◽  
Density Map ◽  
Unit Cell Dimensions ◽  
Electron Density Map

Three crystalline modifications of the bacterial serine peptidase Streptomyces griseus Protease B have been grown. A 4.5 Å resolution electron density map of one form has been computed from the multiple isomorphous replacement (MIR) phases deduced from two heavy metal derivatives plus the anomalous dispersion effects of one of the derivatives. The crystalline modification used was grown from 0.7–1.0 M KH2PO4 at pH 4.2. These crystals have space group P21212 and unit cell dimensions of a = 44.15 (5) Å, b = 108.72 (10) Å, and c = 37.28 (5) Å. The crystal asymmetric unit contains a protein mass of approximately 19 000 daltons. The electron density map, mean figure of merit 0.80, clearly shows the molecular boundary; relatively long stretches of extended chain are discernable. The active site has been identified from a difference electron density map computed using the MIR protein phases and the amplitude differences between a crystal of the enzyme inhibited at the active serine in solution by p-iodobenzenesulfonyl fluoride (PIPSYL) and those from a crystal of the native enzyme. In addition to showing the site of the PIPSYL binding, there is an apparent conformational change in which the histidine side chain moves away from the serine residue by approximately 4.3 Å.

An 11 Å-resolution electron density map of southern bean mosaic virus

1978 ◽  
Vol 34 (2) ◽  
pp. 567-578 ◽  
Author(s):  
I. Rayment ◽  
J. E. Johnson ◽  
D. Suck ◽  
T. Akimoto ◽  
M. G. Rossmann ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Electron Density ◽  
Southern Bean Mosaic Virus ◽  
Resolution Electron ◽  
Density Map ◽  
Electron Density Map

scholarly journals Machine learning to estimate the local quality of protein crystal structures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ikuko Miyaguchi ◽  
Miwa Sato ◽  
Akiko Kashima ◽  
Hiroyuki Nakagawa ◽  
Yuichi Kokabu ◽  
...  
Keyword(s):  
Electron Density ◽  
Protein Structures ◽  
Three Dimensional ◽  
Protein Crystal ◽  
Low Resolution ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Local Quality ◽  
Density Map ◽  
Electron Density Map

AbstractLow-resolution electron density maps can pose a major obstacle in the determination and use of protein structures. Herein, we describe a novel method, called quality assessment based on an electron density map (QAEmap), which evaluates local protein structures determined by X-ray crystallography and could be applied to correct structural errors using low-resolution maps. QAEmap uses a three-dimensional deep convolutional neural network with electron density maps and their corresponding coordinates as input and predicts the correlation between the local structure and putative high-resolution experimental electron density map. This correlation could be used as a metric to modify the structure. Further, we propose that this method may be applied to evaluate ligand binding, which can be difficult to determine at low resolution.

scholarly journals QAEmap: A Novel Local Quality Assessment Method for Protein Crystal Structures Using Machine Learning

2021 ◽  
Author(s):  
Ikuko Miyaguchi ◽  
Miwa Sato ◽  
Akiko Kashima ◽  
Hiroyuki Nakagawa ◽  
Yuichi Kokabu ◽  
...  
Keyword(s):  
High Resolution ◽  
Quality Assessment ◽  
Electron Density ◽  
Protein Structures ◽  
Assessment Method ◽  
Protein Crystal ◽  
Low Resolution ◽  
Density Maps ◽  
Density Map ◽  
Electron Density Map

Abstract Low-resolution electron density maps can pose a major obstacle in the determination and use of protein structures. Herein, we describe a novel method, quality assessment based on an electron density map (QAEmap), that evaluates local protein structures determined by X-ray crystallography and corrects structural errors using low-resolution maps. QAEmap uses a three-dimensional deep convolutional neural network with electron density maps and their corresponding coordinates as input and predicts the correlation between the local structure and the putative high-resolution experimental electron density map. This estimates how well the structure fits the high-resolution map. Further, we propose that this method may be applied to evaluate ligand binding, which can be difficult to determine at low resolution.

scholarly journals The Conformation of the ε- and γ-Subunits within theEscherichia coliF1ATPase

2001 ◽  
Vol 276 (50) ◽  
pp. 47227-47232 ◽  
Author(s):  
Andrew C. Hausrath ◽  
Roderick A. Capaldi ◽  
Brian W. Matthews
Keyword(s):  
Electron Density ◽  
Large Scale ◽  
Coiled Coil ◽  
Water Soluble ◽  
E Coli ◽  
Γ Subunit ◽  
Resolution Electron ◽  
Density Map ◽  
Functional States ◽  
Electron Density Map

F1is the water-soluble portion of the ubiquitous F1F0ATP synthase. Its structure includes three α- and three β-subunits, arranged as a hexameric disc, plus a γ-subunit that penetrates the center of the disc akin to an axle. Recently Hausrathet al.(Hausrath, A. C., Grüber, G., Matthews, B. W., and Capaldi, R. A. (1999)Proc. Natl. Acad. Sci. U. S. A.96, 13697–13702) obtained an electron density map ofE. coliF1at 4.4-Å resolution in which the coiled-coil α-helices of the γ-subunit could be seen to extend 45 Å from the base of the α3β3hexamer. Subsequently the structure of a truncated form of theE. coliγ-subunit in complex with ε has been described (Rodgers, A. J. W., and Wilce, M. C. J. (2000)Nat. Struct. Biol.7, 1051–1054). In the present study the 4.4-Å resolution electron density map ofE. coliF1is re-evaluated in light of the newly available data on the γ- and ε-subunits. It is shown that the map of the F1complex is consistent with the structure of the isolated subunits. WhenE. coliF1is compared with that from beef heart, the structures of theE. coliγ- and ε-subunits are seen to be generally similar to their counterparts in the bovine enzyme but to undergo major shifts in position. In particular, the two long, coiled-coil α-helices that lie along the axis of F1both unwind and rotate. Also the ε-subunit rotates around the axis by 81° and undergoes a net translation of about 23 Å. It is argued that these large-scale changes in conformation reflect distinct functional states that occur during the rotation of the γ-subunit within the α3β3hexamer.

Sign in / Sign up

Export Citation Format

Share Document