Sectioned rubisco crystals in TEM

1990 ◽  
Vol 48 (3) ◽  
pp. 664-665
Author(s):  
Gunnel Karlsson ◽  
Jan-Olov Bovin ◽  
Michael Bosma
Keyword(s):  
Plant Cell ◽  
Carbon Fixation ◽  
Unit Cell ◽  
Protein Crystals ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Photosynthetic Carbon Fixation ◽  
Photosynthetic Carbon

RuBisCO (D-ribulose-l,5-biphosphate carboxylase/oxygenase) is the most aboundant enzyme in the plant cell and it catalyses the key carboxylation reaction of photosynthetic carbon fixation, but also the competing oxygenase reaction of photorespiation. In vitro crystallized RuBisCO has been studied earlier but this investigation concerns in vivo existance of RuBisCO crystals in anthers and leaves ofsugarbeets. For the identification of in vivo protein crystals it is important to be able to determinethe unit cell of cytochemically identified crystals in the same image. In order to obtain the best combination of optimal contrast and resolution we have studied different staining and electron accelerating voltages. It is known that embedding and sectioning can cause deformation and obscure the unit cell parameters.

scholarly journals Cloning, expression, crystallization and crystallographic analysis of CouR fromRhodopseudomonas palustris

2015 ◽  
Vol 71 (11) ◽  
pp. 1416-1420 ◽  
Author(s):  
Chen Pan ◽  
Yong-lin Hu ◽  
Xiang-ning Jiang ◽  
Ying Gai
Keyword(s):  
Rhodopseudomonas Palustris ◽  
Crystallographic Analysis ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Ligand Complex ◽  
Space Group ◽  
Cell Parameters ◽  
Dna Fragment

CouR fromRhodopseudomonas palustrisis a member of the MarR transcriptional regulator family. It regulates the expression of CouA and CouB, enzymes that are involved in the degradation ofp-coumarate.In vivo, CouR binds to a DNA fragment containing thecouABpromoter and suppresses the expression of CouA and CouB, while binding ofp-coumaroyl-CoA attenuates its affinity towards DNA and activates the expression of CouA and CouB. Here, the crystallization and X-ray diffraction analyses of CouR alone and in complex withp-coumaroyl-CoA are reported. Apo and ligand-complexed CouR crystals diffracted to 2.5 and 3.3 Å resolution, respectively. The crystals of apo CouR belonged to space groupP22121, with unit-cell parametersa= 62.78,b = 76.15,c = 87.38 Å, whereas the crystals of the CouR–ligand complex belonged to space groupP212121, with unit-cell parametersa= 61.37,b= 69.82,c = 70.32 Å. The crystals were predicted to contain two CouR molecules or CouR–ligand complexes per asymmetric unit.

Control of photosynthetic carbon fixation and partitioning: how can use of genetically manipulated plants improve the nature and quality of information about regulation?

1993 ◽  
Vol 342 (1301) ◽  
pp. 225-233 ◽  
Keyword(s):  
Molecular Genetics ◽  
Carbon Fixation ◽  
Quality Of Information ◽  
Photosynthetic Carbon Fixation ◽  
Intact Organism ◽  
Photosynthetic Carbon ◽  
Genetically Manipulated ◽  
Traditional Approaches

The study of regulation has previously involved indirect, and largely correlative, approaches. In the following contribution I illustrate the uses and limitations of these traditional approaches, and then discuss how molecular genetics provide a new tool to test directly ideas about regulation in vivo in the intact organism.

scholarly journals Hydrothermal Synthesis of Sr-doped Hydroxyapatite and Its Antibacterial Activity

2019 ◽  
Vol 64 (1) ◽  
pp. 54-60 ◽  
Author(s):  
Teodóra Nagyné-Kovács ◽  
Boglárka Mészáros ◽  
Mónika Molnár ◽  
Mária Tolner ◽  
István Endre Lukács ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
In Vitro Cytotoxicity ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Reaction Conditions ◽  
Cell Parameters ◽  
E Coli ◽  
Lattice Constants ◽  
Sample Characterization

In this study, we prepared hydroxyapatite (HAP) samples using hydrothermal method. We investigated the effect of reaction conditions such as phosphate excess applying 1.49 and 1.67 (as stoichiometric) Ca/P ratio, pH (9/ 10/ 11/ 12) and time (4/ 8/ 12/ 24 h). Sample characterization was carried out by XRD and SEM. The results showed, all samples had HAP structure, however, lower Ca/P ratio, larger reaction time and setting the pH to 10 increased the crystallinity. Then, we synthetized Sr-doped HAP samples, varying the Sr concentration using 2, 4, 6, 8 and 10 % Sr/ (Ca+Sr). The Sr content was revealed by EDX. Sr-incorporation did not change the obtained crystalline HAP phase but the unit cell parameters increased. We calculated lattice constants and found that a, b changed from 9.4310 Å to 9.4700 Å, c from 6.8819 Å to 6.9227 Å and the unit cell volume from 530.0951 Å3 to 537.6556 Å3 due to the larger ionic radius of Sr compared to Ca. The pure and doped samples had uniform, mostly needle-like morphology with 100-300 nm length and 25-100 nm. In vitro cytotoxicity tests revealed evident antibacterial activity in the case of doped samples compared to pure HAP against E. coli.

scholarly journals The SecB-like chaperone Rv1957 fromMycobacterium tuberculosis: crystallization and X-ray crystallographic analysis

2016 ◽  
Vol 72 (6) ◽  
pp. 457-461 ◽  
Author(s):  
Zuokun Lu ◽  
Han Wang ◽  
TingTing Yu
Keyword(s):  
Crystallographic Analysis ◽  
Unfolded Proteins ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Sec Pathway ◽  
Secretion Pathway ◽  
High Concentrations

Protein export is important in all bacteria, and bacteria have evolved specialized export machineries to fulfil this task. InMycobacterium tuberculosis, the causative agent of tuberculosis, the general secretion pathway (Sec pathway) is conserved and is essential in performing the export of proteins. The bacterial Sec pathway post-translationally exports unfolded proteins out of the cytoplasm, and the core of the Sec pathway is composed of a heterotrimeric membrane-embedded channel, SecYEG, and two cytosolic components, SecA and SecB. SecB functions by stabilizing unfolded proteins, maintaining them in an export-competent state. Although SecB is mainly found in Proteobacteria, a SecB-like protein, Rv1957, that controls a stress-response toxin–antitoxin system, is found inM. tuberculosis. Rv1957 can also functionally replace theEscherichia coliSecB chaperone bothin vivoandin vitro. In this work, the production, crystallization and X-ray crystallographic analysis of Rv1957 are reported. Notably, diffraction-quality crystals were obtained only at high concentrations of dimethyl sulfoxide,i.e.about 12%(v/v). The crystals of Rv1957 belonged to space groupP212121, with unit-cell parametersa= 64.5,b= 92.0,c= 115.4 Å.

Kinematical and Dynamical CBED Pattern Models: Increasing the Accuracy of the Unit-Cell Parameter Measurements Based on CBED Patterns

1990 ◽  
Vol 48 (2) ◽  
pp. 540-541
Author(s):  
I.N. Yadhikov ◽  
S.K. Maksimov
Keyword(s):  
Reciprocal Lattice ◽  
Unit Cell ◽  
Reciprocal Lattice Vector ◽  
Unit Cell Parameters ◽  
Lattice Vector ◽  
Cell Parameters ◽  
Accuracy Of Measurements ◽  
The Difference ◽  
Image Position ◽  
Convergent Beam

Convergent beam electron diffraction (CBED) is widely used as a microanalysis tool. By the relative position of HOLZ-lines (Higher Order Laue Zone) in CBED-patterns one can determine the unit cell parameters with a high accuracy up to 0.1%. For this purpose, maps of HOLZ-lines are simulated with the help of a computer so that the best matching of maps with experimental CBED-pattern should be reached. In maps, HOLZ-lines are approximated, as a rule, by straight lines. The actual HOLZ-lines, however, are different from the straights. If we decrease accelerating voltage, the difference is increased and, thus, the accuracy of the unit cell parameters determination by the method becomes lower.To improve the accuracy of measurements it is necessary to give up the HOLZ-lines substitution by the straights. According to the kinematical theory a HOLZ-line is merely a fragment of ellipse arc described by the parametric equationwith arc corresponding to change of β parameter from -90° to +90°, wherevector, h - the distance between Laue zones, g - the value of the reciprocal lattice vector, g‖ - the value of the reciprocal lattice vector projection on zero Laue zone.

On the accuracy of determining the unit cell parameters of single crystals on modern laboratory diffractometers

2021 ◽  
Vol 62 (5) ◽  
Author(s):  
П.C. Серебренникова ◽  
В.Ю. Комаров ◽  
А.С. Сухих ◽  
С.А. Громилов
Keyword(s):  
Single Crystals ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Cell Parameters

scholarly journals Crystal Structure Refinements of Four Monazite Samples from Different Localities

Minerals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1028 ◽  
Author(s):  
M. Mashrur Zaman ◽  
Sytle M. Antao
Keyword(s):  
Crystal Structure ◽  
Electron Probe ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Large Unit Cell ◽  
A Site

This study investigates the crystal chemistry of monazite (APO4, where A = Lanthanides = Ln, as well as Y, Th, U, Ca, and Pb) based on four samples from different localities using single-crystal X-ray diffraction and electron-probe microanalysis. The crystal structure of all four samples are well refined, as indicated by their refinement statistics. Relatively large unit-cell parameters (a = 6.7640(5), b = 6.9850(4), c = 6.4500(3) Å, β = 103.584(2)°, and V = 296.22(3) Å3) are obtained for a detrital monazite-Ce from Cox’s Bazar, Bangladesh. Sm-rich monazite from Gunnison County, Colorado, USA, has smaller unit-cell parameters (a = 6.7010(4), b = 6.9080(4), c = 6.4300(4) Å, β = 103.817(3)°, and V = 289.04(3) Å3). The a, b, and c unit-cell parameters vary linearly with the unit-cell volume, V. The change in the a parameter is large (0.2 Å) and is related to the type of cations occupying the A site. The average <A-O> distances vary linearly with V, whereas the average <P-O> distances are nearly constant because the PO4 group is a rigid tetrahedron.

scholarly journals New crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 in two conformations

2014 ◽  
Vol 70 (11) ◽  
pp. 1468-1471
Author(s):  
Trung Thanh Thach ◽  
Sangho Lee
Keyword(s):  
Crystal Structures ◽  
Adenylate Kinase ◽  
Bound States ◽  
Critical Role ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Ligand Free ◽  
Adenylate Kinases

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groupsP21andP1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space groupC2, with unit-cell parametersa= 73.5,b= 54.3,c= 62.7 Å, β = 118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cαatoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitorP1,P5-bis(adenosine-5′-)pentaphosphate (Ap5A) belonged to space groupP1, with unit-cell parametersa= 53.9,b= 62.3,c= 63.0 Å, α = 101.9, β = 112.6, γ = 89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.

Compressibility of β-As4S4: an in situ high-pressure single-crystal X-ray study

2012 ◽  
Vol 76 (4) ◽  
pp. 963-973 ◽  
Author(s):  
G. O. Lepore ◽  
T. Boffa Ballaran ◽  
F. Nestola ◽  
L. Bindi ◽  
D. Pasqual ◽  
...  
Keyword(s):  
Pressure Range ◽  
Substantial Reduction ◽  
Structural Data ◽  
Unit Cell ◽  
Van Der Waals Interactions ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Intermolecular Distances

AbstractAmbient temperature X-ray diffraction data were collected at different pressures from two crystals of β-As4S4, which were made by heating realgar under vacuum at 295ºC for 24 h. These data were used to calculate the unit-cell parameters at pressures up to 6.86 GPa. Above 2.86 GPa, it was only possible to make an approximate measurement of the unit-cell parameters. As expected for a crystal structure that contains molecular units held together by weak van der Waals interactions, β-As4S4 has an exceptionally high compressibility. The compressibility data were fitted to a third-order Birch–Murnaghan equation of state with a resulting volume V0 = 808.2(2) Å3, bulk modulus K0 = 10.9(2) GPa and K' = 8.9(3). These values are extremely close to those reported for the low-temperature polymorph of As4S4, realgar, which contains the same As4S4 cage-molecule. Structural analysis showed that the unit-cell contraction is due mainly to the reduction in intermolecular distances, which causes a substantial reduction in the unit-cell volume (∼21% at 6.86 GPa). The cage-like As4S4 molecules are only slightly affected. No phase transitions occur in the pressure range investigated.Micro-Raman spectra, collected across the entire pressure range, show that the peaks associated with As–As stretching have the greatest pressure dependence; the S–As–S bending frequency and the As–S stretching have a much weaker dependence or no variation at all as the pressure increases; this is in excellent agreement with the structural data.

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