Structure of buffalo lactoferrin at 2.5 Å resolution using crystals grown at 303 K shows different orientations of the N and C lobes

1999 ◽  
Vol 55 (11) ◽  
pp. 1805-1813 ◽  
Author(s):  
Subramanian Karthikeyan ◽  
Murugan Paramasivam ◽  
Savita Yadav ◽  
Alagiri Srinivasan ◽  
Tej P. Singh
Keyword(s):  
Crystal Structures ◽  
Crystal Form ◽  
Unit Cell ◽  
The Other ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Cell Parameters ◽  
Other Hand ◽  
External Conditions

The structure of buffalo lactoferrin has been determined at 303 K. The crystals belong to orthorhombic space group P212121, with unit-cell parameters a = 77.5, b = 91.0, c = 131.5 Å and Z = 4. The structure has been refined to an R factor of 0.187. The overall structure of the protein is similar to its structure determined at 277 K in a different crystal form. However, the lobe orientations in the two structures differ by 9.0°, suggesting significant inter-lobe flexibility in this family of proteins. The inter-lobe interactions are predominantly hydrophobic and could act as a cushion for a change in orientation under the influence of external conditions. On the other hand, the domain arrangements are found to be similar in 277 and 303 K crystal structures, with orientations differing by 1.5 and 1.0° in the N and C lobes, respectively. The results of these investigations suggest that the increase in temperature helps in the production of better quality crystals.

scholarly journals Expression, purification and crystallization of the phosphate-binding PstS protein fromPseudomonas aeruginosa

2014 ◽  
Vol 70 (7) ◽  
pp. 906-910 ◽  
Author(s):  
Avi Neznansky ◽  
Yarden Opatowsky
Keyword(s):  
Crystal Form ◽  
Phosphate Transport ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Solvent Content ◽  
Space Group ◽  
Cell Parameters ◽  
Crystal Volume

Pseudomonas aeruginosa(PA) infections pose a serious threat to human health. PA is a leading cause of fatal lung infections in cystic fibrosis and immune-suppressed patients, of sepsis in burn victims and of nosocomial infections. An important element in PA virulence is its ability to establish biofilms that evade suppression by the host's immune system and antibiotics. PstS, a periplasmic subunit of the Pst phosphate-transport system of PA, plays a critical role in the establishment of biofilms. In some drug-resistant PA strains, PstS is secreted in large quantities from the bacteria, where it participates in the assembly of adhesion fibres that enhance bacterial virulence. In order to understand the dual function of PstS in biofilm formation and phosphate transport, the crystal structure of PA PstS was determined. Here, the overexpression inEscherichia coliand purification of PA PstS in the presence of phosphate are described. Two crystal forms were obtained using the vapour-diffusion method at 20°C and X-ray diffraction data were collected. The first crystal form belonged to the centred orthorhombic space groupC2221, with unit-cell parametersa= 67.5,b= 151.3,c= 108.9 Å. Assuming the presence of a dimer in the asymmetric unit gives a crystal volume per protein weight (VM) of 2.09 Å3 Da−1and a solvent content of 41%. The second crystal form belonged to the primitive orthorhombic space groupP212121, with unit-cell parametersa= 35.4,b= 148.3,c= 216.7 Å. Assuming the presence of a tetramer in the asymmetric unit gives a crystal volume per protein weight (VM) of 2.14 Å3 Da−1and a solvent content of 42.65%. A pseudo-translational symmetry is present in theP212121crystal form which is consistent with a filamentous arrangement of PstS in the crystal lattice.

scholarly journals Novel Fluoridoaluminates from Ammonothermal Synthesis: Two Modifications of K2AlF5 and the Elpasolite Rb2KAlF6

Inorganics ◽  
2022 ◽  
Vol 10 (1) ◽  
pp. 7
Author(s):  
Christian Bäucker ◽  
Peter Becker ◽  
Keshia J. Morell ◽  
Rainer Niewa
Keyword(s):  
Unit Cell ◽  
The Other ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Orthorhombic Unit Cell ◽  
Space Group ◽  
Cell Parameters ◽  
Group Type

Two new modifications of the pentafluoridoaluminate K2AlF5 were obtained from ammonothermal synthesis at 753 K, 224 MPa and 773 K, 220 MPa, respectively. Both crystallize in the orthorhombic space group type Pbcn, with close metric relations and feature kinked chains of cis-vertex-connected AlF6 octahedra resulting in the Niggli formula ∞1{[AlF2/2eF4/1t]2−}. The differences lie in the number of octahedra necessary for repetition within the chains, which for K2AlF5-2 is realized after four and for K2AlF5-3 after eight octahedra. As a result, the orthorhombic unit cell for K2AlF5-3 is doubled in chain prolongation direction [001] as compared to K2AlF5-2 (1971.18(4) pm versus 988.45(3) pm, respectively), while the unit cell parameters within the other two directions are virtually identical. Moreover, the new elpasolite Rb2KAlF6 is reported, crystallizing in the cubic space group Fm3¯m with a = 868.9(1) pm and obtained under ammonothermal conditions at 723 K and 152 MPa.

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.

Crystallization and preliminary X-ray study of two crystal forms of Klebsiella oxytoca diol dehydratase–cyanocobalamin complex

1999 ◽  
Vol 55 (4) ◽  
pp. 907-909 ◽  
Author(s):  
Jun Masuda ◽  
Tetsuya Yamaguchi ◽  
Takamasa Tobimatsu ◽  
Tetsuo Toraya ◽  
Kyoko Suto ◽  
...  
Keyword(s):  
Klebsiella Oxytoca ◽  
Crystal Form ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Crystal Forms ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Diol Dehydratase ◽  
Replacement Method

Two crystal forms of Klebsiella oxytoca diol dehydratase complexed with cyanocobalamin have been obtained and preliminary crystallographic experiments have been performed. The crystals belong to two different space groups, depending on the crystallization conditions. One crystal (form I) belongs to space group P212121 with unit-cell parameters a = 76.2, b = 122.3, c = 209.6 Å, and diffracts to 2.2 Å resolution using an X-ray beam from a synchrotron radiation source. The other crystal (form II) belongs to space group P21 with unit-cell parameters a = 75.4, b = 132.7, c = 298.8 Å, β = 91.9°, and diffracts to 3.0 Å resolution. For the purpose of structure determination, a heavy-atom derivative search was carried out and some mercuric derivatives were found to be promising. Structure analysis by the multiple isomorphous replacement method is now under way.

scholarly journals Crystallization of two operator complexes from theVibrio choleraeHigBA2 toxin–antitoxin module

2015 ◽  
Vol 71 (2) ◽  
pp. 226-233 ◽  
Author(s):  
San Hadži ◽  
Abel Garcia-Pino ◽  
Kenn Gerdes ◽  
Jurij Lah ◽  
Remy Loris
Keyword(s):  
Vibrio Cholerae ◽  
Crystal Form ◽  
Unit Cell ◽  
Dna Duplexes ◽  
Dna Duplex ◽  
Unit Cell Parameters ◽  
Crystal Forms ◽  
Space Group ◽  
Cell Parameters ◽  
Complex Crystals

The HigA2 antitoxin and the HigBA2 toxin–antitoxin complex fromVibrio choleraewere crystallized in complex with their operator box. Screening of 22 different DNA duplexes led to two crystal forms of HigA2 complexes and one crystal form of a HigBA2 complex. Crystals of HigA2 in complex with a 17 bp DNA duplex belong to space groupP3221, with unit-cell parametersa=b= 94.0,c= 123.7 Å, and diffract to 2.3 Å resolution. The second form corresponding to HigA2 in complex with a 19 bp duplex belong to space groupP43212 and only diffract to 3.45 Å resolution. Crystals of the HigBA2 toxin–antitoxin were obtained in complex with a 31 bp duplex and belonged to space groupP41212, with unit-cell parametersa=b= 113.6,c= 121.1 Å. They diffract to 3.3 Å resolution.

Crystal structure and topological affinities of magbasite, KBaFe3+Mg7Si8O22(OH)2F6: a trellis structure related to amphibole and carpholite

2014 ◽  
Vol 78 (1) ◽  
pp. 29-45 ◽  
Author(s):  
M. D. Welch ◽  
R. H. Mitchell ◽  
A. R. Kampf ◽  
A. R. Chakhmouradian ◽  
D. Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Carbonatite Complex ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Cell Parameters ◽  
Structural Relations ◽  
Final Agreement

AbstractThe crystal structure of magbasite from the Eldor carbonatite complex, Quebec, Canada, has been determined and indicates that the currently accepted formula should be revised to KBaFe3+Mg7Si8O22(OH)2F6. Magbasite is orthorhombic, space group Cmme (Cmma), with unit-cell parameters a 18.9506(3) Å, b 22.5045(3) Å, c 5.2780(1) Å, V 2250.93(6) Å3 (Z = 4). The structure has been solved and refined to final agreement indices R1 = 0.026, wR2 = 0.052, GooF = 1.116 for a total of 2379 unique reflections, and is a new kind of trellis motif related to amphibole and carpholite topologies. An amphibole-like I-beam ‖(100) of edge-sharing octahedrally-coordinated M(1,2,3) sites, which are filled by Mg, is sandwiched between double-chains of SiO4 tetrahedra ‖c. This I-beam is connected to side-ribbons ‖(010) of edge-sharing (Mg,Fe2+)O4(OH,F)2 and Fe3+O4(OH)2 octahedra to form a tunnelled box or trellis structure very like that of carpholite, for which the I-beams are pyroxene-like. K occupies a tunnel site analogous to the A site of amphibole. Ba occupies a cavity site at the corners where the I-beam and side-ribbon meet, and corresponds to the A site of carpholite. The structural relations between magbasite and carpholite are discussed.

The crystal structure of Cu2GeSe3 and the structure-types of the I2-IV-VI3 family of semiconducting compounds

2021 ◽  
Vol 77 (1) ◽  
pp. 158-167
Author(s):  
Analio Dugarte-Dugarte ◽  
Nahum Ramírez Pineda ◽  
Luis Nieves ◽  
José Antonio Henao ◽  
Graciela Díaz de Delgado ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Initial Report ◽  
Space Group ◽  
Cell Parameters ◽  
Semiconducting Compounds ◽  
Bond Valence Model

Almost 50 years after the initial report, the crystal structure of Cu2GeSe3, a I2-IV-VI3 semiconductor, has been revised using modern single-crystal X-ray diffraction data. The structure of this material can be properly described in the monoclinic space group Cc (No. 9) with unit-cell parameters a = 6.7703 (4) Å, b = 11.8624 (5) Å, c = 6.7705 (4) Å, β = 108.512 (6)°, V = 515.62 (5) Å3, Z = 4, rather than in the orthorhombic space group Imm2 (No. 44) with unit-cell parameters a = 11.860 (3), b = 3.960 (1), c = 5.485 (2) Å, V = 257.61 Å3, Z = 2, as originally proposed [Parthé & Garín (1971). Monatsh. Chem. 102, 1197–1208]. Contrary to what was observed in the orthorhombic structure, the distortions of the tetrahedra in the monoclinic structure are consistent with the distortions expected from considerations derived from the bond valence model. A brief revision of the structures reported for the I2-IV-VI3 family of semiconducting compounds (I: Cu, Ag; IV: Si, Ge, Sn; and VI: S, Se, Te) is also presented.

scholarly journals The novel thermostable cellulose-degrading enzyme DtCel5H from Dictyoglomus thermophilum: crystallization and X-ray crystallographic analysis

2018 ◽  
Vol 74 (1) ◽  
pp. 1-5
Author(s):  
Flavia Squeglia ◽  
Rita Berisio ◽  
Alessia Ruggiero
Keyword(s):  
Ammonium Sulfate ◽  
Glycosyl Hydrolase ◽  
Unit Cell ◽  
Structure Stability ◽  
Waste Biomass ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Cell Parameters ◽  
Dictyoglomus Thermophilum

Cellulose-based products constitute the great majority of municipal waste, and applications of cellulases in the conversion of waste biomass to biofuels will be a key technology in future biorefineries. Currently, multi-enzymatic pre-treatment of biomass is a crucial step in making carbohydrates more accessible for subsequent fermentation. Using bioinformatics analysis, endo-β-(1,4)-glucanase from Dictyoglomus thermophilum (DtCel5H) was identified as a new member of glycosyl hydrolase family 5. The gene encoding DtCel5H was cloned and the recombinant protein was overexpressed for crystallization and biophysical studies. Here, it is shown that this enzyme is active on cellulose substrates and is highly thermostable. Crystals suitable for crystallographic investigations were also obtained in different crystallization conditions. In particular, ordered crystals of DtCel5H were obtained using either ammonium sulfate or polyethylene glycol (PEG) as a precipitant agent. The crystals obtained in the presence of ammonium sulfate belonged to space group P32, with unit-cell parameters a = 73.1, b = 73.1, 73.1, c = 127.8 Å, and diffracted to 1.5 Å resolution, whereas the second crystal form belonged to the orthorhombic space group P212121, with unit-cell parameters a = 49.3, b = 67.9, c = 103.7 Å, and diffracted to 1.6 Å resolution. The crystal structure was solved in both space groups using molecular-replacement methods. Structure–activity and structure–stability studies of DtCel5H will provide insights for the design of high-performance enzymes.

scholarly journals Two crystal forms of a helix-rich fatty acid- and retinol-binding protein, Na-FAR-1, from the parasitic nematodeNecator americanus

2012 ◽  
Vol 68 (7) ◽  
pp. 835-838 ◽  
Author(s):  
Mads Gabrielsen ◽  
M. Florencia Rey-Burusco ◽  
Kate Griffiths ◽  
Andrew J. Roe ◽  
Alan Cooper ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Structural Information ◽  
Binding Protein ◽  
Crystal Form ◽  
Blood Feeding ◽  
Unit Cell ◽  
Retinol Binding Protein ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters

Na-FAR-1 is an unusual α-helix-rich fatty acid- and retinol-binding protein fromNecator americanus, a blood-feeding intestinal parasitic nematode of humans. It belongs to the FAR protein family, which is unique to nematodes; no structural information is available to date for FAR proteins from parasites. Crystals were obtained with two different morphologies that corresponded to different space groups. Crystal form 1 exhibited space groupP432 (unit-cell parametersa = b = c = 120.80 Å, α = β = γ = 90°) and diffracted to 2.5 Å resolution, whereas crystal form 2 exhibited space groupF23 (unit-cell parametersa = b = c = 240.38 Å, α = β = γ = 90°) and diffracted to 3.2 Å resolution. Crystal form 2 showed signs of significant twinning.

Molecular and Crystal Structure of Sildenafil Base

2012 ◽  
Vol 67 (5) ◽  
pp. 491-494 ◽  
Author(s):  
Dmitrijs Stepanovs ◽  
Anatoly Mishnev
Keyword(s):  
Crystal Structure ◽  
Erectile Dysfunction ◽  
Crystal Structures ◽  
Unit Cell ◽  
Sildenafil Citrate ◽  
Unit Cell Parameters ◽  
Monoclinic System ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Sildenafil citrate monohydrate, well known as Viagra®, is a drug for the treatment of erectile dysfunction. Here we present the X-ray crystal structure of the sildenafil base, C22H30N6O4S. The compound crystallizes in the monoclinic system, space group P21/c with the unit cell parameters a = 17:273(1), b=17:0710(8), c=8:3171(4) Å , b =99:326(2), Z = 4, V = 2420:0(3) Å3. A comparison with the known crystal structures of sildenafil citrate monohydrate and sildenafil saccharinate is also presented.

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