Crystallization and preliminary structural studies of Scilla campanulata lectin complexed with α1–6 mannobiose

1998 ◽  
Vol 54 (1) ◽  
pp. 90-92 ◽  
Author(s):  
Lisa M Wright ◽  
Stephen D. Wood ◽  
Colin D. Reynolds ◽  
Pierre J. Rizkallah ◽  
Anthony K. Allen
Keyword(s):  
Molecular Replacement ◽  
X Rays ◽  
Synchrotron Source ◽  
Replacement Method ◽  
Cell Dimensions ◽  
Molecular Replacement Method ◽  
Hanging Drop Method ◽  
Unit Cell Dimensions ◽  
Antiretroviral Activity ◽  
Image Plate System

Recent work has shown that Scilla campanulata agglutinin from bluebell bulbs has a strong affinity for α(1,3)- and α(1,6)-linked mannosyl residues and possesses moderate antiretroviral activity. This lectin has been crystallized by the hanging-drop method of vapour diffusion complexed with the disaccharide mannose-α1,6-D-mannose. The crystals are in the space group P21212 with unit-cell dimensions a = 70.63, b = 92.79 and c = 47.25 Å, and with a dimer in the asymmetric unit. The crystals diffract X-rays to beyond 1.5 Å resolution at 277 K and are stable in an X-ray beam. Data to 1.6 Å resolution have been collected using a MAR image-plate system at a synchrotron source and the structure of the complex has been solved by the molecular replacement method.

scholarly journals Structure basis for E2-E3 interaction in the plant Atg conjugation system

2014 ◽  
Vol 70 (a1) ◽  
pp. C1660-C1660
Author(s):  
Kazuaki Matoba ◽  
Yuko Fujioka ◽  
Machiko Sakoh-Nakatogawa ◽  
Hitoshi Nakatogawa ◽  
Yoshinori Ohsumi ◽  
...  
Keyword(s):  
Mutational Analysis ◽  
Membrane Vesicle ◽  
Side Chain ◽  
Molecular Replacement ◽  
X Rays ◽  
Conjugation System ◽  
Intracellular Degradation ◽  
Replacement Method ◽  
Molecular Replacement Method

Autophagy is an intracellular degradation system conserved from yeast to mammal that isolates the cellular materials and organelles into a double membrane vesicle, termed an autophagosome, for degradation. Autophagosome formation depends on Atg8 and Atg12 conjugation systems, which produce Atg8-phosphatidylethanolamine (PE) conjugate as a final product that plays a crucial role for promoting autophagy. Another conjugate, Atg12-Atg5, functions as E3 and promotes transfer of Atg8 from Atg3 (E2) to PE. Here, we identified the minimum binding region of Atg3 for Atg12 by in vitro pull-down assay using Arabidopsis thaliana (At) homologs and crystallized the AtAtg12b-AtAtg3 peptide complex. The obtained crystal (P64, a = 128.5, b = 128.5, c = 163.2 Å) diffracted X-rays to 3.2 Å resolution, and its structure was determined by the molecular replacement method. AtAtg12b forms a swapping dimer in the crystal. The side-chain of AtAtg3 Met157 is bound deeply to the hydrophobic pocket of AtAtg12b consisting of Phe30, Val41, and Phe44. The importance of AtAtg3 Met157 for AtAtg12b binding was confirmed by mutational analysis. These data establish the basis for E2-E3 interaction in the plant Atg system.

Crystallization and preliminary X-ray studies of hORF6, a novel human antioxidant enzyme

1998 ◽  
Vol 54 (3) ◽  
pp. 436-436 ◽  
Author(s):  
Hee-Jeong Choi ◽  
Sang Won Kang ◽  
Chul-Hak Yang ◽  
Sue Goo Rhee ◽  
Seong-Eon Ryu
Keyword(s):  
Antioxidant Enzyme ◽  
Unit Cell ◽  
X Rays ◽  
Asymmetric Unit ◽  
Data Set ◽  
X Ray ◽  
Space Groups ◽  
Cell Dimensions ◽  
Hanging Drop Method ◽  
Unit Cell Dimensions

HORF6 is a member of the novel antioxidant enzyme family found in humans. A recombinant form of hORF6 expressed and purified from E. coli has been crystallized by the hanging-drop method using various PEG's as precipitating agents. HORF6 crystallizes in two different monoclinic space groups, P21 and C2. The P21 crystals have unit-cell dimensions of a = 47.85, b = 75.17, c = 63.30 Å and β = 110.21° and contain two monomers per asymmetric unit, while the C2 crystals have unit-cell dimensions of a = 165.27, b = 95.44, c = 166.44 Å and β = 128.97° and contain more than six monomers per asymmetric unit. The P21 crystals with the smaller unit cell diffract X-rays better and behave well for the X-ray analysis. A native data set from a single crystal of the P21 space group gas been collected to 2.0 Å resolution.

Crystallization and preliminary X-ray diffraction studies of human catalase

1999 ◽  
Vol 55 (9) ◽  
pp. 1614-1615 ◽  
Author(s):  
R. A. P. Nagem ◽  
E. A. L. Martins ◽  
V. M. Gonçalves ◽  
R. Aparício ◽  
I. Polikarpov
Keyword(s):  
Search Model ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Beef Liver ◽  
X Ray ◽  
Diffusion Technique ◽  
Cell Dimensions ◽  
Synchrotron Radiation Diffraction ◽  
Replacement Solution ◽  
Unit Cell Dimensions

The enzyme catalase (H2O2–H2O2 oxidoreductase; E.C. 11.1.6) was purified from haemolysate of human placenta and crystallized using the vapour-diffusion technique. Synchrotron-radiation diffraction data have been collected to 1.76 Å resolution. The enzyme crystallized in the space group P212121, with unit-cell dimensions a = 83.6, b = 139.4, c = 227.5 Å. A molecular-replacement solution of the structure has been obtained using beef liver catalase (PDB code 4blc) as a search model.

scholarly journals Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF fromMicrocystis aeruginosa, a putative reductase participating in aeruginosin biosynthesis

2015 ◽  
Vol 71 (4) ◽  
pp. 466-470 ◽  
Author(s):  
Ruyi Ding ◽  
Cui Xu ◽  
Xu Chen ◽  
Mengyun Bao ◽  
Xiaoting Qiu
Keyword(s):  
Diffraction Analysis ◽  
Biosynthetic Pathway ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Antithrombotic Activity ◽  
X Ray ◽  
Cell Parameters ◽  
Maximum Resolution ◽  
Replacement Method ◽  
Molecular Replacement Method

The 2-carboxy-6-hydroxyoctahydroindole moiety is an essential residue for the antithrombotic activity of aeruginosins, which are a class of cyanobacteria-derived bioactive linear tetrapeptides. The biosynthetic pathway of the 2-carboxy-6-hydroxyoctahydroindole moiety has not yet been resolved. AerF was indicated to be involved in the biosynthesis of the 2-carboxy-6-hydroxyoctahydroindole moiety. This study reports the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF fromMicrocystis aeruginosawith a C-terminal His6tag. The crystal diffracted to a maximum resolution of 1.38 Å and belonged to the tetragonal space groupP4322, with unit-cell parametersa=b= 101.581,c= 116.094 Å. The calculated Matthews coefficient and solvent content of the crystal were 2.47 Å3 Da−1and 50.32%, respectively. The initial model of the structure was obtained by the molecular-replacement method and refinement of the structure is in progress.

scholarly journals Crystallization and preliminary X-ray crystallographic analysis of PBPD2 fromListeria monocytogenes

2014 ◽  
Vol 70 (4) ◽  
pp. 535-537 ◽  
Author(s):  
Hyung Jin Cha ◽  
Jae-Hee Jeong ◽  
Yeon-Gil Kim
Keyword(s):  
Biosynthetic Pathway ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Low Molecular Weight ◽  
Molecular Replacement ◽  
Orthorhombic Space Group ◽  
Penicillin Binding Proteins ◽  
Cell Parameters ◽  
Replacement Method ◽  
Molecular Replacement Method

Penicillin-binding proteins (PBPs), which mediate the peptidoglycan biosynthetic pathway in the bacterial cell wall, have been intensively investigated as a target for the design of antibiotics. In this study, PBPD2, a low-molecular-weight PBP encoded bylmo2812fromListeria monocytogenes, was overexpressed inEscherichia coli, purified and crystallized at 295 K using the sitting-drop vapour-diffusion method. The crystal belonged to the primitive orthorhombic space groupP212121, with unit-cell parametersa= 37.7,b= 74.7,c= 75.1 Å, and diffracted to 1.55 Å resolution. There was one molecule in the asymmetric unit. The preliminary structure was determined by the molecular-replacement method.

X-Ray Powder Diffraction (XRPD)

2016 ◽  
pp. 326-341 ◽  
Author(s):  
Robert Heimann
Keyword(s):  
Powder Diffraction ◽  
X Rays ◽  
Powder Diffraction File ◽  
Thin Beam ◽  
Archaeological Ceramics ◽  
X Ray ◽  
Analytical Technique ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

X-ray powder diffraction (XRPD) is an important tool to determine the phase composition of archaeological ceramics. In principle, a thin beam of X-rays incident to a lattice plane of crystalline matter is scattered in specific directions and angles depending on the distances of atoms. This allows determination of characteristic unit cell dimensions and serves to unambiguously identify crystalline phases in the ceramics. In this chapter, generation of X-rays and the theory of diffraction will be briefly discussed as well as equipment, focusing conditions, and sample preparation procedures of common XRPD methods. The X-ray pattern obtained will provide an analytical fingerprint that can be matched against the Powder Diffraction File of the International Centre for Diffraction Data. Examples will be given of application of this analytical technique to archaeological clays and ceramics.

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