Crystallization and Preliminary X-ray Diffraction Analysis of Cold-Active β-Galactosidase from Arthrobacter sp. C2-2

2005 ◽  
Vol 70 (1) ◽  
pp. 124-132 ◽  
Author(s):  
Hana Petroková ◽  
Eva Vondráčková ◽  
Tereza Skálová ◽  
Jan Dohnálek ◽  
Petra Lipovová ◽  
...  
Keyword(s):  
Structure Refinement ◽  
Monoclinic Space Group ◽  
Molecular Replacement ◽  
Phase Problem ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Psychrotrophic Bacteria ◽  
Cold Active

β-Galactosidase from psychrotrophic bacteria strainArthrobactersp. C2-2 catalyzes cleavage of β-D-galactosyl moieties from β-D-galactosides and is interesting for its activity at low temperatures. Various types of crystals with dimensions of up to 0.8 mm were obtained and X-ray diffraction data up to 1.9 Å were collected. The crystals belong to the monoclinic space groupP21with unit-cell parametersa= 140.1 Å,b= 205.7 Å,c= 140.5 Å and β = 102.3°. The enzyme (molecular weight of a monomer is 111 kDa) forms hexamers in the crystal structure (one hexamer per asymmetric unit). The phase problem was solved by molecular replacement. Structure refinement is in progress.

scholarly journals Purification and crystallographic analysis of a FAD-dependent halogenase fromStreptomycessp. JCM9888

2015 ◽  
Vol 71 (8) ◽  
pp. 972-976 ◽  
Author(s):  
Yanqun Zhao ◽  
Baohua Yan ◽  
Ting Yang ◽  
Jian Jiang ◽  
Heng Wei ◽  
...  
Keyword(s):  
Model Building ◽  
Structure Refinement ◽  
Crystallographic Analysis ◽  
Monoclinic Space Group ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Hexahistidine Tag ◽  
Crystallization Experiments

A new FAD (flavin adenine dinucleotide)-dependent halogenase HalY fromStreptomycessp. JCM9888 was reported to be involved in the regioselective halogenation of adenine. HalY is a variant B FAD-dependent halogenase that is most similar to the halogenase PltA involved in pyoluteorin biosynthesis. This study reports the overexpression and purification of HalY with an N-terminal hexahistidine tag, followed by crystallization experiments and X-ray crystallographic analysis. HalY was purified as a monomer in solution and crystallized to give X-ray diffraction to a resolution of 1.7 Å. The crystal belonged to the monoclinic space groupP21, with unit-cell parametersa= 41.4,b= 113.4,c= 47.6 Å, α = γ = 90, β = 107.4°, and contained one monomer of HalY in the asymmetric unit, with a calculated Matthews coefficient of 2.3 Å3 Da−1and a solvent content of 46%. The structure of the halogenase CndH was used as a search model in molecular replacement to obtain the initial model of HalY. Manual model building and structure refinement of HalY are in progress.

Arrheniusite-(Ce), CaMg[(Ce7Y3)Ca5](SiO4)3(Si3B3O18)(AsO4)(BO3)F11, a New Member of the Vicanite Group, from the Östanmossa Mine, Norberg, Sweden

2021 ◽  
Author(s):  
Dan Holtstam ◽  
Luca Bindi ◽  
Paola Bonazzi ◽  
Hans-Jürgen Förster ◽  
Ulf B. Andersson
Keyword(s):  
Structure Refinement ◽  
New Mineral ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Calculated Density ◽  
Epma Data ◽  
X Ray ◽  
Cell Parameters ◽  
Greenish Yellow ◽  
The Ideal

ABSTRACT Arrheniusite-(Ce) is a new mineral (IMA 2019-086) from the Östanmossa mine, one of the Bastnäs-type deposits in the Bergslagen ore region, Sweden. It occurs in a metasomatic F-rich skarn, associated with dolomite, tremolite, talc, magnetite, calcite, pyrite, dollaseite-(Ce), parisite-(Ce), bastnäsite-(Ce), fluorbritholite-(Ce), and gadolinite-(Nd). Arrheniusite-(Ce) forms anhedral, greenish-yellow translucent grains, exceptionally up to 0.8 mm in diameter. It is optically uniaxial (–), with ω = 1.750(5), ε = 1.725(5), and non-pleochroic in thin section. The calculated density is 4.78(1) g/cm3. Arrheniusite-(Ce) is trigonal, space group R3m, with unit-cell parameters a = 10.8082(3) Å, c = 27.5196(9) Å, and V = 2784.07(14) Å3 for Z = 3. The crystal structure was refined from X-ray diffraction data to R1 = 3.85% for 2286 observed reflections [Fo > 4σ(Fo)]. The empirical formula for the fragment used for the structural study, based on EPMA data and results from the structure refinement, is: (Ca0.65As3+0.35)Σ1(Mg0.57Fe2+0.30As5+0.10Al0.03)Σ1[(Ce2.24Nd2.13La0.86Gd0.74Sm0.71Pr0.37)Σ7.05(Y2.76Dy0.26Er0.11Tb0.08Tm0.01Ho0.04Yb0.01)Σ3.27Ca4.14]Σ14.46(SiO4)3[(Si3.26B2.74)Σ6O17.31F0.69][(As5+0.65Si0.22P0.13)Σ1O4](B0.77O3)F11; the ideal formula obtained is CaMg[(Ce7Y3)Ca5](SiO4)3(Si3B3O18)(AsO4)(BO3)F11. Arrheniusite-(Ce) belongs to the vicanite group of minerals and is distinct from other isostructural members mainly by having a Mg-dominant, octahedrally coordinated site (M6); it can be considered a Mg-As analog to hundholmenite-(Y). The threefold coordinated T5 site is partly occupied by B, like in laptevite-(Ce) and vicanite-(Ce). The mineral name honors C.A. Arrhenius (1757–1824), a Swedish officer and chemist, who first discovered gadolinite-(Y) from the famous Ytterby pegmatite quarry.

scholarly journals A putative siderophore-interacting protein from the marine bacteriumShewanella frigidimarinaNCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

2016 ◽  
Vol 72 (9) ◽  
pp. 667-671 ◽  
Author(s):  
Inês B. Trindade ◽  
Bruno M. Fonseca ◽  
Pedro M. Matias ◽  
Ricardo O. Louro ◽  
Elin Moe
Keyword(s):  
Iron Acquisition ◽  
Crystallographic Analysis ◽  
Monoclinic Space Group ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Interacting Protein ◽  
X Ray ◽  
Cell Parameters ◽  
Unit Structure ◽  
Shewanella Frigidimarina

Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacteriumShewanella frigidimarinaNCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space groupP21, with unit-cell parametersa= 48.04,b= 78.31,c= 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.

Clino-suenoite, a newly approved magnesium-iron-manganese amphibole from Valmalenco, Sondrio, Italy

2018 ◽  
Vol 82 (1) ◽  
pp. 189-198
Author(s):  
Roberta Oberti ◽  
Massimo Boiocchi ◽  
Frank C. Hawthorne ◽  
Marco E. Ciriotti ◽  
Olav Revheim ◽  
...  
Keyword(s):  
Microprobe Analysis ◽  
Electron Microprobe Analysis ◽  
Structure Refinement ◽  
Type Specimen ◽  
Crystal Structure Refinement ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Iron Manganese

ABSTRACTClino-suenoite, ideally □${\rm Mn}_{2}^{2 +} $Mg5Si8O22(OH)2 is a new amphibole of the magnesium-iron-manganese subgroup of the amphibole supergroup. The type specimen was found at the Lower Scerscen Glacier, Valmalenco, Sondrio, Italy, where it occurs in Mn-rich quartzite erratics containing braunite, rhodonite, spessartine, carbonates and various accessory minerals. The empirical formula derived from electron microprobe analysis and single-crystal structure refinement is: ANa0.04B(${\rm Mn}_{1.58}^{2 +} $Ca0.26Na0.16)Σ2.00C(Mg4.21${\rm Mn}_{0. 61}^{2 +} {\rm Fe}_{0.04}^{2 +} $Zn0.01Ni0.01${\rm Fe}_{0.08}^{3 +} $Al0.04)Σ5.00TSi8.00O22W[(OH1.94F0.06)]Σ=2.00. Clino-suenoite is biaxial (+), with α = 1.632(2), β = 1.644(2), γ = 1.664(2) and 2Vmeas. = 78(2)° and 2Vcalc. = 76.3°. The unit-cell parameters in the C2/m space group are a = 9.6128(11), b = 18.073(2), c = 5.3073(6) Å, β = 102.825(2)° and V = 899.1(2) Å3 with Z = 2. The strongest ten reflections in the powder X-ray diffraction pattern [d (in Å), I, (hkl)] are: 2.728, 100, (151); 2.513, 77, ($\bar 2$02); 3.079, 62, (310); 8.321, 60, (110); 3.421, 54, (131); 2.603, 42, (061); 2.175, 42, (261); 3.253, 41, (240); 2.969, 40, (221); 9.036, 40, (020).

scholarly journals Crystallization and preliminary X-ray diffraction studies of guanidinoacetate methyltransferase from rat liver

1999 ◽  
Vol 55 (11) ◽  
pp. 1928-1929 ◽  
Author(s):  
Junichi Komoto ◽  
Yafei Huang ◽  
Yongbo Hu ◽  
Yoshimi Takata ◽  
Kiyoshi Konishi ◽  
...  
Keyword(s):  
Rat Liver ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Guanidinoacetate methyltransferase is the enzyme which catalyzes the last step of creatine biosynthesis. The enzyme is found ubiquitously and in abundance in the livers of all vertebrates. Recombinant rat-liver guanidinoacetate methyltransferase has been crystallized with guanidinoacetate and S-adenosylhomocysteine. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 54.8, b = 162.5, c = 56.1 Å, β = 96.8 (1)° at 93 K, and typically diffract beyond 2.8 Å.

Molecular and crystal structure of a copper(II) complex of sildenafil

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Akhmatkhodja N. Yunuskhodjayev ◽  
Shokhista F. Iskandarova ◽  
Vahobjon Kh. Sabirov
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Piperazine Ring ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Abstract The crystal structure of a copper(II) complex of protonated sildenafil, CuCl3C22H31N6O4S⋅2H2O was studied by single crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P21/n with the unit cell parameters a = 15.4292(2), b = 9.06735(12), c = 21.1752(2) Å, V = 2945.48(7) Å3, Z = 4. The Cu atom is coordinated by the sildenafil ligand via the N2 atom of the pyrazolopyrimidine ring and by three chloride anions. Sildenafil is protonated at the methylated N6 atom of the piperazine ring and it is cation ligand with a 1+ charge.

scholarly journals Purification and X-ray crystallographic analysis of 7-keto-8-aminopelargonic acid (KAPA) synthase fromMycobacterium smegmatis

2014 ◽  
Vol 70 (10) ◽  
pp. 1372-1375 ◽  
Author(s):  
Shanghua Fan ◽  
Defeng Li ◽  
Joy Fleming ◽  
Yuan Hong ◽  
Tao Chen ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Essential Enzyme ◽  
Mycobacterial Growth

7-Keto-8-aminopelargonic acid synthase (KAPA synthase; BioF) is an essential enzyme for mycobacterial growth that catalyses the first committed step in the biotin-synthesis pathway. It is a pyridoxal 5′-phosphate (PLP)-dependent enzyme and is a potential drug target. Here, the cloning, expression, purification and crystallization of KAPA synthase fromMycobacterium smegmatis(MsBioF) and the characterization of MsBioF crystals using X-ray diffraction are described. The crystals diffracted to 2.3 Å resolution and belonged to the monoclinic space groupP21, with unit-cell parametersa= 70.88,b= 91.68,c= 109.84 Å, β = 97.8°. According to the molecular weight of MsBioF, the unit-cell parameters and the self-rotation function map, four molecules are present in each asymmetric unit with aVMvalue of 2.06 Å3 Da−1and a solvent content of 40.20%.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of the BRPF1 bromodomain in complex with its H2AK5ac and H4K12ac histone-peptide ligands

2014 ◽  
Vol 70 (10) ◽  
pp. 1389-1393 ◽  
Author(s):  
Mulu Y. Lubula ◽  
Amanda Poplawaski ◽  
Karen C. Glass
Keyword(s):  
Diffraction Analysis ◽  
National Laboratory ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Direct Role ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

The bromodomain-PHD finger protein 1 (BRPF1) is an essential subunit of the monocytic leukemia zinc (MOZ) histone acetyltransferase (HAT) complex and is required for complex formation and enzymatic activation. BRPF1 contains a structurally conserved bromodomain, which recognizes specific acetyllysine residues on histone proteins. The MOZ HAT plays a direct role in hematopoiesis, and deregulation of its activity is linked to the development of acute myeloid leukemia. However, the molecular mechanism of histone-ligand recognition by the BRPF1 bromodomain is currently unknown. The 117-amino-acid BRPF1 bromodomain was overexpressed inEscherichia coliand purified to homogeneity. Crystallization experiments of the BRPF1 bromodomain in complex with its H4K12ac and H2AK5ac histone ligands yielded crystals that were suitable for high-resolution X-ray diffraction analysis. The BRPF1 bromodomain–H4K12ac crystals belonged to the tetragonal space groupP43212, with unit-cell parametersa= 75.1,b= 75.1,c= 86.3 Å, and diffracted to a resolution of 1.94 Å. The BRPF1 bromodomain–H2AK5ac crystals grew in the monoclinic space groupP21, with unit-cell parametersa= 60.9,b= 55.6,c= 82.1 Å, β = 93.6°, and diffracted to a resolution of 1.80 Å. Complete data sets were collected from both crystal forms using synchrotron radiation on beamline X29 at Brookhaven National Laboratory (BNL).

scholarly journals Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of a ferredoxin/flavodoxin-NADP(H) oxidoreductase (Bc0385) fromBacillus cereus

2014 ◽  
Vol 70 (6) ◽  
pp. 777-780 ◽  
Author(s):  
Silje Skråmo ◽  
Hans-Petter Hersleth ◽  
Marta Hammerstad ◽  
K. Kristoffer Andersson ◽  
Åsmund K. Røhr
Keyword(s):  
Electron Transfer ◽  
Thioredoxin Reductase ◽  
Free Form ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters

Ferredoxin/flavodoxin-NADP(H) oxidoreductases (FNRs) are key enzymes involved in catalysing electron transfer between ferredoxins/flavodoxins and NAD(P)H/NAD(P)+. InBacillus cereusthere are three genes that may encode FNRs, and the Bc0385 FNR has been cloned, overexpressed, purified and successfully crystallized in its NADPH/NADP+-free form. Diffraction data have been collected to 2.5 Å resolution from crystals belonging to the orthorhombic space groupP21212, with unit-cell parametersa= 57.2,b= 164.3,c= 95.0 Å, containing two FNR molecules in the asymmetric unit. The structure of the Bc0385 FNR has been solved by molecular replacement, and is a member of the homodimeric thioredoxin reductase-like class of FNRs.

Synthesis and X-ray diffraction data of dichlorodioxido (4,4-dimethoxycarbonyl-2,2′-bipyridyl) molybdenum(VI)

2013 ◽  
Vol 29 (1) ◽  
pp. 42-45 ◽  
Author(s):  
H.A. Camargo ◽  
N.J. Castellanos ◽  
C.C. Rosas ◽  
J.A. Henao
Keyword(s):  
Unit Cell ◽  
Monoclinic Space Group ◽  
Crystalline Compound ◽  
X Ray Diffraction ◽  
Molybdenum Complex ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Green Solution ◽  
Xrpd Pattern

The dichlorodioxido(4,4′-dimethoxycarbonyl-2,2′-bipyridyl)molybdenum(VI) complex was prepared from molybdenum(VI) dichloride dioxide and 4,4-dimethoxycarbonyl-2,2-bipyridyl in CH2Cl2 obtaining a clear green solution. The molybdenum complex was separated by precipitation with ethyl ether. The XRPD pattern for the new compound showed that the crystalline compound belongs to the monoclinic space group P21/c (No 14) with refined unit-cell parameters a = 12.104(1) Å, b = 14.933 (2) Å, c = 11.010 (2) Å and ß = 115.409° (9). The volume of the unit cell is V = 1797.6 (3) Å3.

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