Structures of native, substrate-bound and inhibited forms ofMycobacterium tuberculosisimidazoleglycerol-phosphate dehydratase

2013 ◽  
Vol 69 (12) ◽  
pp. 2461-2467 ◽  
Author(s):  
Mohammad Syed Ahangar ◽  
Rajan Vyas ◽  
Nazia Nasir ◽  
Bichitra K. Biswal
Keyword(s):  
Functional Form ◽  
Tertiary Structure ◽  
Point Group ◽  
Three Dimensional ◽  
Imidazole Ring ◽  
Group Symmetry ◽  
Biosynthesis Pathway ◽  
Histidine Biosynthesis ◽  
Unique Structural Feature ◽  
Β Sheets

Imidazoleglycerol-phosphate dehydratase (IGPD; HisB), which catalyses the conversion of imidazoleglycerol-phosphate (IGP) to imidazoleacetol-phosphate in the histidine biosynthesis pathway, is absent in mammals. This feature makes it an attractive target for herbicide discovery. Here, the crystal structure ofMycobacterium tuberculosis(Mtb) IGPD is reported together with the first crystal structures of substrate-bound and inhibited (by 3-amino-1,2,4-triazole; ATZ) forms of IGPD from any organism. The overall tertiary structure ofMtbIGPD, a four-helix-bundle sandwiched between two four-stranded mixed β-sheets, resembles the three-dimensional structures of IPGD from other organisms; however,MtbIGPD possesses a unique structural feature: the insertion of a one-turn 310-helix followed by a loop ten residues in length. The functional form of IGPD is 24-meric, exhibiting 432 point-group symmetry. The structure of the IGPD–IGP complex revealed that the imidazole ring of the IGP is firmly anchored between the two Mn atoms, that the rest of the substrate interacts through hydrogen bonds mainly with residues Glu21, Arg99, Glu180, Arg121 and Lys184 which protrude from three separate protomers and that the 24-mer assembly contains 24 catalytic centres. Both the structural and the kinetic data demonstrate that the inhibitor 3-amino-1,2,4-triazole inhibits IGPD competitively.

scholarly journals Point-group symmetry detection in three-dimensional charge density of biomolecules

2019 ◽  
Vol 36 (7) ◽  
pp. 2237-2243
Author(s):  
Cyril F Reboul ◽  
Simon Kiesewetter ◽  
Dominika Elmlund ◽  
Hans Elmlund
Keyword(s):  
Charge Density ◽  
Single Particle ◽  
Statistical Tests ◽  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Point Group Symmetry ◽  
Density Maps ◽  
Point Groups ◽  
Density Map

Abstract Motivation No rigorous statistical tests for detecting point-group symmetry in three-dimensional (3D) charge density maps obtained by electron microscopy (EM) and related techniques have been developed. Results We propose a method for determining the point-group symmetry of 3D charge density maps obtained by EM and related techniques. Our ab initio algorithm does not depend on atomic coordinates but utilizes the density map directly. We validate the approach for a range of publicly available single-particle cryo-EM datasets. In straightforward cases, our method enables fully automated single-particle 3D reconstruction without having to input an arbitrarily selected point-group symmetry. When pseudo-symmetry is present, our method provides statistics quantifying the degree to which the 3D density agrees with the different point-groups tested. Availability and implementation The software is freely available at https://github.com/hael/SIMPLE3.0.

scholarly journals Crystal structure of the coordination polymer [FeIII2{PtII(CN)4}3]

2015 ◽  
Vol 71 (1) ◽  
pp. i1-i2
Author(s):  
Maksym Seredyuk ◽  
M. Carmen Muñoz ◽  
José A. Real ◽  
Turganbay S. Iskenderov
Keyword(s):  
Crystal Structure ◽  
Coordination Polymer ◽  
Point Group ◽  
Three Dimensional ◽  
Title Complex ◽  
Group Symmetry ◽  
Point Group Symmetry ◽  
Rotation Axes ◽  
Square Planar ◽  
Cyanide Ligands

The title complex, poly[dodeca-μ-cyanido-diiron(III)triplatinum(II)], [FeIII2{PtII(CN)4}3], has a three-dimensional polymeric structure. It is built-up from square-planar [PtII(CN)4]2−anions (point group symmetry 2/m) bridging cationic [FeIIIPtII(CN)4]+∞layers extending in thebcplane. The FeIIatoms of the layers are located on inversion centres and exhibit an octahedral coordination sphere defined by six N atoms of cyanide ligands, while the PtIIatoms are located on twofold rotation axes and are surrounded by four C atoms of the cyanide ligands in a square-planar coordination. The geometrical preferences of the two cations for octahedral and square-planar coordination, respectively, lead to a corrugated organisation of the layers. The distance between neighbouring [FeIIIPtII(CN)4]+∞layers corresponds to the lengtha/2 = 8.0070 (3) Å, and the separation between two neighbouring PtIIatoms of the bridging [PtII(CN)4]2−groups corresponds to the length of thecaxis [7.5720 (2) Å]. The structure is porous with accessible voids of 390 Å3per unit cell.

scholarly journals Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3

2015 ◽  
Vol 71 (3) ◽  
pp. 251-253 ◽  
Author(s):  
Nataliia Yu. Strutynska ◽  
Marina A. Bondarenko ◽  
Ivan V. Ogorodnyk ◽  
Vyacheslav N. Baumer ◽  
Nikolay S. Slobodyanik
Keyword(s):  
Crystal Structure ◽  
High Temperature ◽  
Point Group ◽  
Three Dimensional ◽  
Type Structure ◽  
Group Symmetry ◽  
Site Symmetry ◽  
Point Group Symmetry ◽  
Crystallization Method ◽  
Temperature Crystallization

Potassium rubidium cobalt(II)/titanium(IV) tris(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/TiIV)O6octahedra (point group symmetry .3.) and PO4tetrahedra. The K+and Rb+cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms.

scholarly journals Crystal structures of two alkaline earth (M= Ba and Sr) dimanganese(II) iron(III) tris(orthophosphates)

2017 ◽  
Vol 73 (5) ◽  
pp. 767-770
Author(s):  
Ghaleb Alhakmi ◽  
Abderrazzak Assani ◽  
Mohamed Saadi ◽  
Lahcen El Ammari
Keyword(s):  
Crystal Structures ◽  
Alkaline Earth ◽  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Solid State Reactions ◽  
Site Symmetry ◽  
Orthorhombic System ◽  
Group Type ◽  
Alkaline Earth Cations

Two new orthophosphates, BaMn2Fe(PO4)3[barium dimanganese(II) iron(III) tris(orthophosphate)] and SrMn2Fe(PO4)3[strontium dimanganese(II) iron(III) tris(orthophosphate)], were synthesized by solid-state reactions. They are isotypic and crystallize in the orthorhombic system with space group typePbcn. Their crystal structures comprise infinite zigzag chains of edge-sharing FeO6octahedra (point group symmetry .2.) and Mn2O10double octahedra running parallel to [001], linked by two types of PO4tetrahedra. The so-formed three-dimensional framework delineates channels running along [001], in which the alkaline earth cations (site symmetry .2.) are located within a neighbourhood of eight O atoms.

scholarly journals Crystal structure of tetrakis(μ3-2-{[1,1-bis(hydroxymethyl)-2-oxidoethyl]iminomethyl}phenolato)tetracopper(II) ethanol monosolvate 2.5-hydrate

2015 ◽  
Vol 71 (5) ◽  
pp. m116-m117
Author(s):  
Weilun Wang ◽  
Jingwen Ran
Keyword(s):  
Rotation Axis ◽  
Point Group ◽  
Solvent Molecule ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Hydrogen Bond Interactions ◽  
Water Solvent ◽  
Phenol Hydroxy Group ◽  
Solvent Molecules ◽  
Hydroxy Groups

The title compound, [Cu4(C11H13NO4)4]·CH3CH2OH·2.5H2O, is an electronically neutral tetranuclear copper(II) complex with a cubane-like Cu4O4core. The complete molecule has point group symmetry 2. The phenol hydroxy group and one of the three alcohol hydroxy groups of each 2-{[tris(hydroxymethyl)methyl]iminomethyl}phenol ligand are deprotonated, while the secondary amine and the other two hydroxy groups remain unchanged. The CuIIatoms in the Cu4O4core are connected by four μ3-O atoms from the deprotonated alcohol hydroxy groups. Each of the pentacoordinated CuIIions has an NO4distorted square-pyramidal environment through coordination to the tridentate Schiff base ligands. The Cu—N/O bond lengths span the range 1.902 (4)–1.955 (4) Å, similar to values reported for related structures. There are O—H...O hydrogen-bond interactions between the complex molecules and the ethanol and water solvent molecules, leading to the formation of a three-dimensional network. The ethanol solvent molecule is disordered about a twofold rotation axis. One of the two independent water molecules is also located on this twofold rotation axis and shows half-occupancy.

scholarly journals Crystal structure of alluaudite-type NaMg3(HPO4)2(PO4)

2015 ◽  
Vol 71 (7) ◽  
pp. 813-815 ◽  
Author(s):  
Ahmed Ould Saleck ◽  
Abderrazzak Assani ◽  
Mohamed Saadi ◽  
Cyrille Mercier ◽  
Claudine Follet ◽  
...  
Keyword(s):  
Point Group ◽  
Three Dimensional ◽  
The Other ◽  
Group Symmetry ◽  
Strong Hydrogen Bond ◽  
Site Symmetry ◽  
Point Group Symmetry ◽  
Hydrogen Phosphate ◽  
Hydrothermal Conditions ◽  
Different Types

The title compound, sodium trimagnesium bis(hydrogen phosphate) phosphate, was obtained under hydrothermal conditions. In the crystal, two types of [MgO6] octahedra, one with point group symmetry 2, share edges to build chains extending parallel to [10-1]. These chains are linked together by two kinds of phosphate tetrahedra, HPO4and PO4, the latter with point group symmetry 2. The three-dimensional framework delimits two different types of channels extending along [001]. One channel hosts the Na+cations (site symmetry 2) surrounded by eight O atoms, with Na—O bond lengths varying between 2.2974 (13) and 2.922 (2) Å. The OH group of the HPO4tetrahedron points into the other type of channel and exhibits a strong hydrogen bond to an O atom of the PO4tetrahedron on the opposite side.

scholarly journals Crystal structures of Sr(ClO4)2·3H2O, Sr(ClO4)2·4H2O and Sr(ClO4)2·9H2O

2014 ◽  
Vol 70 (12) ◽  
pp. 510-514 ◽  
Author(s):  
Erik Hennings ◽  
Horst Schmidt ◽  
Wolfgang Voigt
Keyword(s):  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Water Molecules ◽  
Point Group Symmetry ◽  
Rotation Axes ◽  
Dimensional Network ◽  
Tricapped Trigonal Prism ◽  
Trigonal Prismatic Coordination ◽  
Solid Liquid

The title compounds, strontium perchlorate trihydrate {di-μ-aqua-aquadi-μ-perchlorato-strontium, [Sr(ClO4)2(H2O)3]n}, strontium perchlorate tetrahydrate {di-μ-aqua-bis(triaquadiperchloratostrontium), [Sr2(ClO4)4(H2O)8]} and strontium perchlorate nonahydrate {heptaaquadiperchloratostrontium dihydrate, [Sr(ClO4)2(H2O)7]·2H2O}, were crystallized at low temperatures according to the solid–liquid phase diagram. The structures of the tri- and tetrahydrate consist of Sr2+cations coordinated by five water molecules and four O atoms of four perchlorate tetrahedra in a distorted tricapped trigonal–prismatic coordination mode. The asymmetric unit of the trihydrate contains two formula units. Two [SrO9] polyhedra in the trihydrate are connected by sharing water molecules and thus forming chains parallel to [100]. In the tetrahydrate, dimers of two [SrO9] polyhedra connected by two sharing water molecules are formed. The structure of the nonahydrate contains one Sr2+cation coordinated by seven water molecules and by two O atoms of two perchlorate tetrahedra (point group symmetry ..m), forming a tricapped trigonal prism (point group symmetrym2m). The structure contains additional non-coordinating water molecules, which are located on twofold rotation axes. O—H...O hydrogen bonds between the water molecules as donor and ClO4tetrahedra and water molecules as acceptor groups lead to the formation of a three-dimensional network in each of the three structures.

scholarly journals Crystal structure of bis(4-acetylanilinium) tetrachloridomercurate(II)

2015 ◽  
Vol 71 (12) ◽  
pp. m236-m237
Author(s):  
Manickam Thairiyaraja ◽  
Arumugam Elangovan ◽  
Ganesh Arivazhagan ◽  
Kuthambalam Selvaraju ◽  
Subbiah Thamotharan
Keyword(s):  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Dimensional Network ◽  
Centroid Distance ◽  
Bonding Interaction ◽  
Benzene Rings ◽  
Π Stacking Interaction ◽  
Considerable Distortion ◽  
Tetrahedral Anion

The structure of the title salt, (C8H10NO)2[HgCl4], is isotypic with that of the cuprate(II) and cobaltate(II) analogues. The asymmetric unit contains one 4-acetylanilinium cation and one half of a tetrachloridomercurate(II) anion (point group symmetrym). The Hg—Cl distances are in the range 2.4308 (7)–2.5244 (11) Å and the Cl—Hg—Cl angles in the range of 104.66 (2)–122.94 (4)°, indicating a considerable distortion of the tetrahedral anion. In the crystal, cations are linked by an intermolecular N—H...O hydrogen-bonding interaction, leading to aC(8) chain motif with the chains extending parallel to thebaxis. There is also a π–π stacking interaction with a centroid-to-centroid distance of 3.735 (2) Å between neighbouring benzene rings along this direction. The anions lie between the chains and interact with the cations through intermolecular N—H...Cl hydrogen bonds, leading to the formation of a three-dimensional network structure.

scholarly journals Crystal structure of Ag2(μ-SCN)2(NH3)4

2016 ◽  
Vol 72 (7) ◽  
pp. 881-883 ◽  
Author(s):  
Thomas G. Müller ◽  
Florian Kraus
Keyword(s):  
Crystal Structure ◽  
Liquid Ammonia ◽  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Hydrogen Bonding Interactions ◽  
Dimensional Network ◽  
Binuclear Molecule ◽  
Thiocyanate Ligand ◽  
Argentophilic Interactions

Di-μ-thiocyanato-bis[diamminesilver(I)], [Ag2(μ-SCN)2(NH3)4], was synthesized by the reaction of AgSCN with anhydrous liquid ammonia. In the binuclear molecule, the AgIatom is coordinated by two ammine ligands and the S atom of one thiocyanate ligand. Two of these [Ag(SCN)(NH3)2] units are bridged by the S atoms of the thiocyanate anions at longer distances, leading to a dimer with point group symmetryC2. The distance between the AgIatoms in the dimer is at 3.0927 (6) Å within the range of argentophilic interactions. The crystal structure displays N—H...N and N—H...S hydrogen-bonding interactions that build up a three-dimensional network.

scholarly journals Crystal structure of an unknown solvate of bis(tetra-n-butylammonium) [N,N′-(4-trifluoromethyl-1,2-phenylene)bis(oxamato)-κ4O,N,N′,O′]nickelate(II)

2015 ◽  
Vol 71 (6) ◽  
pp. 578-581
Author(s):  
François Eya'ane Meva ◽  
Dieter Schaarschmidt ◽  
Tobias Rüffer
Keyword(s):  
Rotation Axis ◽  
Point Group ◽  
Solvent Molecule ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Acta Cryst ◽  
Coordination Environment ◽  
Dimensional Network ◽  
Square Planar ◽  
The Given

In the title compound, [N(C4H9)4]2[Ni(C11H3F3N2O6)] or [N(n-Bu)4]2[Ni(topbo)] [n-Bu =n-butyl and topbo = 4-trifluoromethyl-1,2-phenylenebis(oxamate)], the Ni2+cation is coordinated by two deprotonated amido N atoms and two carboxylate O atoms, setting up a slightly distorted square-planar coordination environment. The [Ni(topbo]2−anion lies on a twofold rotation axis. Due to an incompatibility with the point-group symmetry of the complete molecule, orientational disorder of the CF3group is observed. The tetrahedral ammonium cations and the anion are linked by weak intermolecular C—H...O and C—H...F hydrogen-bonding interactions into a three-dimensional network. A region of electron density was treated with the SQUEEZE procedure inPLATON[Spek (2015).Acta Cryst. C71, 9–18] following unsuccessful attempts to model it as plausible solvent molecule(s). The given chemical formula and other crystal data do not take into account the unknown solvent molecule.

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