Polymorphous crystallization and diffraction of threonine deaminase from Escherichia coli

1998 ◽  
Vol 54 (3) ◽  
pp. 467-469 ◽  
Author(s):  
D. Travis Gallagher ◽  
Edward Eisenstein ◽  
Kathryn E. Fisher ◽  
James Zondlo ◽  
Diana Chinchilla ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Diffraction Data ◽  
Crystal Form ◽  
Data Sets ◽  
Threonine Deaminase ◽  
Crystal Forms ◽  
Space Group ◽  
Regulatory Functions

The biosynthetic threonine deaminase from Escherichia coli, an allosteric tetramer with key regulatory functions, has been crystallized in several crystal forms. Two distinct forms, both belonging to either space group P3121 or P3221, with different sized asymmetric units that both contain a tetramer, grow under identical conditions. Diffraction data sets to 2.8 Å resolution (native) and 2.9 Å resolution (isomorphous uranyl derivative) have been collected from a third crystal form in space group I222.

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.

Preparation and Crystal Structures of the Isotypic Compounds CdXO4 · 2 HgO (X = S, Se)

2004 ◽  
Vol 59 (3) ◽  
pp. 281-285 ◽  
Author(s):  
Matthias Weil
Keyword(s):  
Single Crystals ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Building Blocks ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
Space Group ◽  
X Ray ◽  
Structure Factors

Colourless single crystals of the compounds CdXO4 · 2 HgO (X = S, Se) were obtained under hydrothermal conditions (250 °C, 5 d), starting from stoichiometric amounts of HgO, CdSO4 ·7H2O and CdSeO4 ·2H2O, respectively. The crystal structures were determined from X-ray diffraction data sets. The CdXO4 · 2HgO compounds crystallise isotypically with two formula units in space group P1̅ (# 2) [CdSO4 · 2HgO (CdSeO4 · 2HgO): a = 6.793(2) (6.9097(5)) Å , b = 7.205(2) (7.1786(6)) Å , c=7.359(2) (7.4556(6)) Å ,α =73.224(6) (74.586(2))°, β =66.505(6) (68.229(1))°, γ =63.054(5) (63.886(1))°, 1670 (1786) structure factors, 92 parameters, R[F2 > 2σ(F2)] = 0.0379 (0.0244)] and are made up from zig-zag [O-Hg-O]∞ chains with very short bonds of d̅(Hg-O) 2.025 Å , distorted [CdO6] octahedra (d̅(Cd-O)= 2.297 Å ), and XO4 tetrahedra (d̅(S-O)= 1.458 Å , d̅(Se-O)= 1.633 Å ) as the main building blocks. The CdXO4 ·2HgO compounds reveal no structural relationship with the corresponding HgXO4 ·2HgO phases

scholarly journals Preliminary crystallographic analysis of the N-terminal domain of FILIA, a protein essential for embryogenesis

2010 ◽  
Vol 66 (9) ◽  
pp. 1111-1114
Author(s):  
Juke Wang ◽  
Tong-Cun Zhang ◽  
Xinqi Liu
Keyword(s):  
Diffraction Data ◽  
Early Stage ◽  
Crystal Form ◽  
Crystallographic Analysis ◽  
Orthorhombic Crystal ◽  
Crystal Forms ◽  
Terminal Domain ◽  
Peg 4000 ◽  
Tetragonal Crystals ◽  
Crystallization Conditions

FILIA is a component of the subcortical maternal complex that is essential for early stage embryogenesis. Its 6×His-tagged N-terminal domain was expressed inEscherichia coliand purified to homogeneity. Two types of crystals formed under different crystallization conditions during screening. Orthorhombic crystals appeared in a solution containing 1.4 Mammonium sulfate, 0.1 MTris pH 8.2 and 12% glycerol, while tetragonal crystals were obtained using 15% PEG 4000 mixed with 0.1 MHEPES pH 7.5 and 15% 2-propanol. High-quality diffraction data were collected from the two crystal forms to resolutions of 1.8 and 2.2 Å, respectively, using synchrotron radiation. The Matthews coefficients indicated that theP212121andP41212 crystals contained two molecules and one molecule per asymmetric unit, respectively. A selenomethionine-substituted sample failed to crystallize under the native conditions, but another orthorhombic crystal form was obtained under different conditions and anomalous diffraction data were collected.

scholarly journals Use of a novel microtitration protocol to obtain diffraction-quality crystals of 4-hydroxy-2-oxoglutarate aldolase fromBos taurus

2014 ◽  
Vol 70 (11) ◽  
pp. 1546-1549 ◽  
Author(s):  
Amadeus Huang ◽  
Edward Baker ◽  
Kerry Loomes
Keyword(s):  
Primary Hyperoxaluria ◽  
Crystal Form ◽  
Coding Region ◽  
Crystal Forms ◽  
Space Group ◽  
X Ray Crystallography ◽  
Primary Hyperoxaluria Type 3 ◽  
Type 3 ◽  
Purification Protocol ◽  
Hyperoxaluria Type

The enzyme 4-hydroxy-2-oxoglutarate aldolase (HOGA) catalyses the retro-aldol degradation of 4-hydroxy-2-oxoglutarate to pyruvate and glyoxylate as part of the hydroxyproline catabolic pathway in mammals. Mutations in the coding region of the human HOGA gene are associated with primary hyperoxaluria type 3, a disease characterized by excessive oxalate production and ultimately stone deposition. Native HOGA was purified from bovine kidney using an improved and streamlined purification protocol from which two crystal forms were obtained using two different approaches. Vapour diffusion using PEG 3350 as a precipitant produced monoclinic crystals that belonged to space groupC2 and diffracted to 3.5 Å resolution. By comparison, orthorhombic crystals belonging to space groupI222 orI212121and diffracting to beyond 2.25 Å resolution were obtained using a novel microtitration protocol with ammonium sulfate. The latter crystal form displayed superior diffraction quality and was suitable for structural determination by X-ray crystallography.

Crystallization and preliminary X-ray analysis of thiaminase I from Bacillus thiaminolyticus: space group change upon freezing of crystals

1998 ◽  
Vol 54 (3) ◽  
pp. 448-450 ◽  
Author(s):  
Nino Campobasso ◽  
Jakob Begun ◽  
Colleen A. Costello ◽  
Tadhg P. Begley ◽  
Steven E. Ealick
Keyword(s):  
Sodium Acetate ◽  
Crystal Form ◽  
Unit Cell ◽  
Diffusion Method ◽  
Crystal Forms ◽  
Space Group ◽  
X Ray ◽  
Cell Dimensions ◽  
Thiaminase I ◽  
Unit Cell Dimensions

Thiaminase I (Mr = 42 100) from B. thiaminolyticus, expressed in E. coli, has been crystallized by the vapor-diffusion method. Three crystal forms, two of which grew from 0.1 M sodium acetate (pH = 4.6), 0.2 M ammonium sulfate and 30%(w/v) PEG 2000, have been examined by X-ray analysis. One crystal form diffracted to 2.5 Å at room temperature, was orthorhombic, and had unit-cell edges of a = 87.7, b = 120.5 and c = 76.7 Å with space group P212121. A self-Patterson map showed a strong peak indicating noncrystallographic translational pseudosymmetry with (u, v, w) = (0.03, 0.0, 0.5). When these crystals were frozen at liquid-nitrogen temperatures, a second crystal form was observed which had unit-cell dimensions a = 85.5, b = 117.5 and c = 36.6 Å with space group P21212. A third crystal form grew from 0.1 M Tris (pH = 8.5), 0.2 M sodium acetate trihydrate and 28%(w/v) PEG 6000 to produce orthorhombic crystals of space group P212121 with cell edges of a = 114.4, b = 123.1 and c = 92.5 Å.

scholarly journals Crystallization and preliminary X-ray diffraction analysis ofHypocrea jecorinaCel7A in two new crystal forms

2014 ◽  
Vol 70 (6) ◽  
pp. 773-776 ◽  
Author(s):  
Annette M. Bodenheimer ◽  
Matthew J. Cuneo ◽  
Paul D. Swartz ◽  
Junhong He ◽  
Hugh M. O'Neill ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Crystal Form ◽  
Unit Cell ◽  
Carbohydrate Binding ◽  
X Rays ◽  
Cellobiohydrolase I ◽  
Unit Cell Parameters ◽  
Crystal Forms ◽  
Space Group ◽  
Cell Parameters

Cel7A (previously known as cellobiohydrolase I) fromHypocrea jecorinawas crystallized in two crystalline forms, neither of which have been previously reported. Both forms co-crystallize under the same crystallization conditions. The first crystal form belonged to space groupC2, with unit-cell parametersa= 152.5,b= 44.9,c= 57.6 Å, β = 101.2°, and diffracted X-rays to 1.5 Å resolution. The second crystal form belonged to space groupP6322, with unit-cell parametersa=b≃ 155,c≃ 138 Å, and diffracted X-rays to 2.5 Å resolution. The crystals were obtained using full-length Cel7A, which consists of a large 434-residue N-terminal catalytic domain capable of cleaving cellulose, a 27-residue flexible linker and a small 36-residue C-terminal carbohydrate-binding module (CBM). However, a preliminary analysis of the electron-density maps suggests that the linker and CBM are disordered in both crystal forms. Complete refinement and structure analysis are currently in progress.

Expression, crystallization and preliminary X-ray analysis of ligand-free human glutathione S-transferase M2–2

1998 ◽  
Vol 54 (3) ◽  
pp. 458-460 ◽  
Author(s):  
Larysa N. Patskovska ◽  
Alexander A. Fedorov ◽  
Yury V. Patskovsky ◽  
Steven C. Almo ◽  
Irving Listowsky
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Asymmetric Unit ◽  
Glutathione S Transferase ◽  
Crystal Forms ◽  
Space Group ◽  
X Ray ◽  
Ligand Free ◽  
Catalytically Active ◽  
Insight Into

Human glutathione-S-transferase M2–2 (hGSTM2–2) was expressed in Escherichia coli and purified by GSH-affinity chromatography. The recombinant enzyme and the protein isolated from human tissue were indistinguishable based on physicochemical, enzymatic and immunological criteria. The catalytically active dimeric hGSTM2–2 was crystallized without GSH or other active-site ligands in two crystal forms. Diffraction from form A crystals extends to 2.5 Å and is consistent with the space group P21 (a = 53.9, b = 81.5, c = 55.6 Å, β = 109.26 Å) with two monomers in the asymmetric unit. Diffraction from form B crystals extends to 3 Å and is consistent with a space group P212121 (a = 57.2, b = 80.7, c = 225.9 Å) with two dimers in the asymmetric unit. This is the first report of ligand-free mu-class GST crystals, and a comparison with liganded complexes will provide insight into the structural consequences of substrate binding which are thought to be important for catalysis.

Disorder and twin refinement of RNA heptamer double helices

1999 ◽  
Vol 55 (8) ◽  
pp. 1405-1413 ◽  
Author(s):  
Uwe Mueller ◽  
Yves A. Muller ◽  
Regine Herbst-Irmer ◽  
Mathias Sprinzl ◽  
Udo Heinemann
Keyword(s):  
Escherichia Coli ◽  
Base Pair ◽  
Molecular Orientation ◽  
Molecular Models ◽  
Rna Structures ◽  
Base Pairs ◽  
Thermal Displacement ◽  
Crystal Forms ◽  
Space Group ◽  
Double Helices

An RNA helix with seven base pairs which was derived from the acceptor stem of Escherichia coli tRNAAla, rGGGGCUA·rUAGCUCC (ALAwt), as well as a variant, rGGGGCUA·rUAGCCCC (ALAC70), in which the single G·U wobble base pair of ALAwt was replaced by G·C, crystallize in space group C2. Both non-isomorphic crystal forms display a complex packing pattern, which can be described alternatively as disorder or pseudo-merohedral twinning. The structure of ALAwt was determined by SIRAS phasing using an isomorphous iodine derivative, rGGGGCi5UA·rUAGCUCC (ALAI). All three RNA structures were subsequently subjected to twin refinement in space group P1, using anisotropic thermal displacement parameters at resolutions of 1.16, 1.23 and 1.4 Å for ALAwt, ALAI and ALAC70, respectively. Alternatively, the structure of ALAwt was refined in space group C2 assuming twofold disorder of the molecular orientation. The refined structures are of reasonable quality according to all available indicators. There are no systematic differences between the molecular models resulting from twin refinement and disorder refinement.

scholarly journals Monitoring protein precipitates by in-house X-ray powder diffraction

2013 ◽  
Vol 28 (S2) ◽  
pp. S458-S469 ◽  
Author(s):  
Kenny Ståhl ◽  
Christian G. Frankær ◽  
Jakob Petersen ◽  
Pernille Harris
Keyword(s):  
Powder Diffraction ◽  
Protein Crystal ◽  
Data Sets ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Parameters ◽  
X Ray Scattering ◽  
Source Organism ◽  
Peak Asymmetry ◽  
Overlapping Peaks

Powder diffraction from protein powders using in-house diffractometers is an effective tool for identification and monitoring of protein crystal forms and artifacts. As an alternative to conventional powder diffractometers a single crystal diffractometer equipped with an X-ray micro-source can be used to collect powder patterns from 1 µl samples. Using a small-angle X-ray scattering (SAXS) camera it is possible to collect data within minutes. A streamlined program has been developed for the calculation of powder patterns from pdb-coordinates, and includes correction for bulk-solvent. A number of such calculated powder patterns from insulin and lysozyme have been included in the powder diffraction database and successfully used for search-match identification. However, the fit could be much improved if peak asymmetry and multiple bulk-solvent corrections were included. When including a large number of protein data sets in the database some problems can be foreseen due to the large number of overlapping peaks in the low-angle region, and small differences in unit cell parameters between pdb-data and powder data. It is suggested that protein entries are supplied with more searchable keywords as protein name, protein type, molecular weight, source organism etc. in order to limit possible hits.

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