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1.  Preliminary X-ray analysis of twinned crystals of sarcosine dimethylglycine methyltransferase from Halorhodospira halochoris  
The crystallization and preliminary X-ray diffraction analysis of sarcosine dimethylglycine methyltransferase from H. halochoris is reported.
Sarcosine dimethylglycine methyltransferase (EC 2.1.1.157) is an enzyme from the extremely halophilic anaerobic bacterium Halorhodospira halochoris. This enzyme catalyzes the twofold methylation of sarcosine to betaine, with S-­adenosylmethionine (AdoMet) as the methyl-group donor. This study presents the crystallization and preliminary X-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in Escherichia coli. Mass spectroscopy was used to determine the purity and homogeneity of the enzyme material. Two different crystal forms, which initially appeared to be hexagonal and tetragonal, were obtained. However, on analyzing the diffraction data it was discovered that both crystal forms were pseudo-merohedrally twinned. The true crystal systems were monoclinic and orthorhombic. The monoclinic crystal diffracted to a maximum of 2.15 Å resolution and the orthorhombic crystal diffracted to 1.8 Å resolution.
doi:10.1107/S1744309109026232
PMCID: PMC2720339  PMID: 19652345
sarcosine dimethylglycine methyltransferase; Halorhodospira halochoris; twinning
2.  Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein tyrosine phosphatase γ in three different crystal forms 
The design, expression and purification of receptor protein tyrosine phosphatase γ and two mutants and their crystallization in three different crystal forms are described.
Protein tyrosine phosphatase γ is a membrane-bound receptor and is designated RPTPγ. RPTPγ and two mutants, RPTPγ(V948I, S970T) and RPTPγ(C858S, S970T), were recombinantly expressed and purified for X-ray crystallographic studies. The purified enzymes were crystallized using the hanging-drop vapor-diffusion method. Crystallographic data were obtained from several different crystal forms in the absence and the presence of inhibitor. In this paper, a description is given of how three different crystal forms were obtained that were used with various ligands. An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form was only obtained in the presence of a particularly elaborated inhibitor.
doi:10.1107/S1744309111017209
PMCID: PMC3144792  PMID: 21795790
protein tyrosine phosphatases; hydrolases; inhibitor complexes
3.  Crystallization and preliminary X-ray diffraction analysis of transaldolase from Thermoplasma acidophilum  
The transaldolase enzyme from T. acidophilum has been crystallized in two different space groups.
The metabolic enzyme transaldolase from Thermoplasma acidophilum was recombinantly expressed in Escherichia coli and could be crystallized in two polymorphic forms. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 6000 as precipitant. Native data sets for crystal forms 1 and 2 were collected in-house to resolutions of 3.0 and 2.7 Å, respectively. Crystal form 1 belonged to the orthorhombic space group C2221 with five monomers per asymmetric unit and crystal form 2 belonged to the monoclinic space group P21 with ten monomers per asymmetric unit.
doi:10.1107/S1744309111009274
PMCID: PMC3087646  PMID: 21543867
Schiff bases; (α/β)8-barrel; fructose 6-phosphate; aldolases; pentose phosphate pathway
4.  Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase 
A case of imperfect pseudo-merohedral twinning in monoclinic crystals of fungal fatty acid synthase is discussed. A space-group transition during crystal dehydration resulted in a Moiré pattern-like interference of the twinned diffraction patterns.
The recent high-resolution structures of fungal fatty acid synthase (FAS) have provided new insights into the principles of fatty acid biosynthesis by large multifunctional enzymes. The crystallographic phase problem for the 2.6 MDa fungal FAS was initially solved to 5 Å resolution using two crystal forms from Thermomyces lanuginosus. Monoclinic crystals in space group P21 were obtained from orthorhombic crystals in space group P212121 by dehydration. Here, it is shown how this space-group transition induced imperfect pseudo-merohedral twinning in the monoclinic crystal, giving rise to a Moiré pattern-like interference of the two twin-related reciprocal lattices. The strategy for processing the twinned diffraction images and obtaining a quantitative analysis is presented. The twinning is also related to the packing of the molecules in the two crystal forms, which was derived from self-rotation function analysis and molecular-replacement solutions using a low-resolution electron microscopy map as a search model.
doi:10.1107/S0907444909000778
PMCID: PMC2631638  PMID: 19171964
imperfect pseudo-merohedral twinning; fungal fatty acid synthase
5.  Determining the structure of a benzene7.2-silicalite-1 zeolite using a single-crystal X-ray method 
An orthorhombic benzene-silicalite-1 single crystal was obtained from a monoclinic twin crystal, and the structure was determined by a single-crystal method for the first time.
A simple method for preparing orthorhombic single crystals of benzene-silicalite-1 was developed. A silicalite-1 crystal was pressed with a weight of 2 g along the +c and −c crystallographic axes while the temperature was increased to 473 K. The temperature was then slowly reduced to 313 K, and these heating and cooling steps were repeated three times. After the orthorhombic single crystals adsorbed benzene, the crystal structure of the resulting benzene-silicalite-1 was determined. There were two kinds of benzene molecules in the asymmetric unit. One was located at the intersection of the straight channels and the sinusoidal channels with the benzene ring parallel to the ac plane. The other benzene was located in the middle of the straight channel.
doi:10.1107/S0108768111038560
PMCID: PMC3222141  PMID: 22101540
ZSM-5; MFI; silicalite-1; benzene-silicalite-1
6.  Purification, crystallization and preliminary crystallographic study of low oxygen-affinity haemoglobin from cat (Felis silvestris catus) in two different crystal forms 
Preliminary studies were carried out to purify and crystallize the sample from cat (Felis silvestris catus), a low oxygen-affinity haemoglobin in different crystal forms.
Haemoglobin is a metalloprotein which plays a major role in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs. The present work reports the preliminary crystallographic study of low oxygen-affinity haemoglobin from cat in different crystal forms. Cat blood was collected, purified by anion-exchange chromatography and crystallized in two different conditions by the hanging-drop vapour-diffusion method under unbuffered low-salt and buffered high-salt concentrations using PEG 3350 as a precipitant. Intensity data were collected using MAR345 and MAR345dtb image-plate detector systems. Cat haemoglobin crystallizes in monoclinic and orthorhombic crystal forms with one and two whole biological molecules (α2β2), respectively, in the asymmetric unit.
doi:10.1107/S1744309109004503
PMCID: PMC2650469  PMID: 19255493
haemoglobin; low oxygen affinity
7.  Crystallization of Escherichia coli maltoporin in the trigonal space group R3 
The crystallization of E. coli maltoporin in a new crystal form that diffracts to high resolution is reported.
Maltoporin is an outer-membrane protein that forms a β-barrel composed of three monomers and ensures the transport of maltose and maltodextrin in Gram-negative bacteria. Previously, the crystallization of Escherichia coli or Salmonella typhimurium maltoporin has been achieved in the presence of a mixture of the detergents β-decylmaltoside and dodecyl nonaoxyethylene. These crystals all belonged to the orthorhombic space group C2221 and gave rise to several structures of maltoporin in complex with different carbohydrates determined at resolutions between 3.2 and 2.4 Å. Here, the crystallization of E. coli maltoporin in a new crystal form is reported; the crystals belonged to the trigonal R3 space group and diffracted to 1.9 Å resolution. These crystals were obtained using n-dodecyl-β-d-maltoside as a detergent. Crystals with a lens or pyramidal morphology could be obtained using sitting or hanging drops, respectively, and despite their very different shapes they presented the same space group and very similar unit-cell parameters.
doi:10.1107/S1744309110047305
PMCID: PMC3079987  PMID: 21206039
outer-membrane proteins; maltoporin; carbohydrates
8.  Crystallization and preliminary X-ray analysis of the O-carbamoyltransferase NovN from the novobiocin-biosynthetic cluster of Streptomyces spheroides  
Crystals of NovN, an O-carbamoyltransferase from S. spheroides, were obtained in monoclinic and orthorhombic forms and native X-ray data were recorded to a maximum of 2.3 Å resolution.
Crystals of recombinant NovN, an O-carbamoyltransferase from Streptomyces spheroides, were grown by vapour diffusion. The protein crystallized in two different crystal forms. Crystal form I belonged to space group C2 and native data were collected to 2.9 Å resolution in-house. Crystal form II had I-centred orthorhombic symmetry and native data were recorded to a resolution of 2.3 Å at a synchrotron. NovN catalyses the final step in the biosynthesis of the aminocoumarin antibiotic novobiocin that targets the essential bacterial enzyme DNA gyrase.
doi:10.1107/S1744309108030145
PMCID: PMC2581686  PMID: 18997325
NovN; O-carbamoyltransferases; Streptomyces; novobiocin; antibiotic biosynthesis
9.  Crystallization and initial X-ray diffraction studies of scaffolding protein (gp7) of bacteriophage ϕ29 
ϕ29 bacteriophage scaffolding protein (gp7) has been overproduced in E. coli, purified, crystallized and characterized by X-ray diffraction. Two distinct crystal forms were obtained and a diffraction data set was collected to 1.8 Å resolution.
The Bacillus subtilis bacteriophage ϕ29 scaffolding protein (gp7) has been crystallized by the hanging-drop vapour-diffusion method at 293 K. Two new distinct crystal forms that both differed from a previously crystallized and solved scaffolding protein were grown under the same conditions. Form I belongs to the primitive tetragonal space group P41212, with unit-cell parameters a = b = 77.13, c = 37.12 Å. Form II crystals exhibit an orthorhombic crystal form, with space group C222 and unit-cell parameters a = 107.50, b = 107. 80, c = 37.34 Å. Complete data sets have been collected to 1.78 and 1.80 Å for forms I and II, respectively, at 100 K using Cu Kα X-rays from a rotating-anode generator. Calculation of a V M value of 2.46 Å3 Da−1 for form I suggests the presence of one molecule in the asymmetric unit, corresponding to a solvent content of 50.90%, whereas form II has a V M of 4.80 Å3 Da−1 with a solvent content of 48.76% and two molecules in the asymmetric unit. The structures of both crystal forms are being determined by the molecular-replacement method using the coordinates of the published crystal structure of gp7.
doi:10.1107/S1744309105008511
PMCID: PMC1952437  PMID: 16511059
scaffolding protein; bacteriophage ϕ29
10.  Crystallization and initial X-ray diffraction studies of the flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from the soil bacterium Paracoccus denitrificans  
The flavin-dependent enzyme FerB from P. denitrificans has been purified and both native and SeMet-substituted FerB have been crystallized. The two variants crystallized in two different crystallographic forms belonging to the monoclinic space group P21 and the orthorhombic space group P21212, respectively. X-ray diffraction data were collected to 1.75 Å resolution for both forms.
The flavin-dependent enzyme FerB from Paracoccus denitrificans reduces a broad range of compounds, including ferric complexes, chromate and most notably quinones, at the expense of the reduced nicotinamide adenine dinucleotide cofactors NADH or NADPH. Recombinant unmodified and SeMet-substituted FerB were crystallized under similar conditions by the hanging-drop vapour-diffusion method with microseeding using PEG 4000 as the precipitant. FerB crystallized in several different crystal forms, some of which diffracted to approximately 1.8 Å resolution. The crystals of native FerB belonged to space group P21, with unit-cell parameters a = 61.6, b = 110.1, c = 65.2 Å, β = 118.2° and four protein molecules in the asymmetric unit, whilst the SeMet-substituted form crystallized in space group P21212, with unit-cell parameters a = 61.2, b = 89.2, c = 71.5 Å and two protein molecules in the asymmetric unit. Structure determination by the three-wavelength MAD/MRSAD method is now in progress.
doi:10.1107/S1744309110005099
PMCID: PMC2852337  PMID: 20383015
flavoenzymes; quinone reductases; Paracoccus denitrificans
11.  Crystallization and preliminary X-ray diffraction studies on the human Plk1 Polo-box domain in complex with an unphosphorylated and a phosphorylated target peptide from Cdc25C 
Crystals of the human Plk1 Polo-box domain in complex with a Cdc25C target peptide in an unphosphorylated and a phosphorylated state have been obtained in orthorhombic and monoclinic forms that diffract to 2.1 and 2.85 Å, respectively, using synchrotron radiation.
Polo-like kinase (Plk1) is crucial for cell-cycle progression via mitosis. Members of the Polo-like kinase family are characterized by the presence of a C-terminal domain termed the Polo-box domain (PBD) in addition to the N-terminal kinase domain. The PBD of Plk1 was cloned and overexpressed in Escherichia coli. Crystallization experiments of the protein in complex with an unphosphorylated and a phosphorylated target peptide from Cdc25C yield crystals suitable for X-­ray diffraction analysis. Crystals of the PBD in complex with the phosphorylated peptide belong to the orthorhombic space group P212121, with unit-cell parameters a = 38.23, b = 67.35, c = 88.25 Å, α = γ = β = 90°, and contain one molecule per asymmetric unit. Crystals of the PBD in complex with the unphosphorylated peptide belong to the monoclinic space group P21, with unit-cell parameters a = 40.18, b = 49.17, c = 56.23 Å, α = γ = 90, β = 109.48°, and contain one molecule per asymmetric unit. The crystals diffracted to resolution limits of 2.1 and 2.85 Å using synchrotron radiation at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS), respectively.
doi:10.1107/S1744309106007494
PMCID: PMC2222578  PMID: 16582488
Polo-like kinase; Polo-box domain; Cdc25C
12.  Peering at a Buried Polymer-Crystal Interface: Probing Heterogeneous Nucleation by Sum Frequency Generation Vibrational Spectroscopy 
Sum frequency generation vibrational spectroscopy (SFG-VS) has been applied to investigate the selective crystallization of two forms of acetaminophen (ACM) on polymer surfaces. To our knowledge this is the first account of SFG-VS being applied to study a polymer-crystal interface. SFG elucidates the molecular level interactions governing phase selection at this buried interface, providing insight to the process of polymer-induced heteronucleation (PIHn) in solution as well as from the vapor phase. ACM heteronucleates from supersaturated aqueous solution in the metastable orthorhombic crystal form, on poly(methyl methacrylate) (PMMA) surfaces, whereas the thermodynamically stable monoclinic crystal form is observed to form on poly(n-butyl methacrylate) (PBMA) surfaces. When the ACM crystals were grown by sublimation, only the monoclinic form was observed on both PMMA and PBMA. SFG-VS results indicate that hydrogen bonds are formed between PMMA C=O groups and the orthorhombic ACM crystals at the PMMA-ACM interface. At PBMA-monoclinic ACM interfaces, no hydrogen bond formation was observed. This research demonstrates that SFG-VS can be used to probe molecular interactions at the polymer-crystal interfaces. Understanding the interfacial molecular interactions will ultimately provide a rational basis to improve methods for polymorph discovery and selection based on heteronucleation on polymer surfaces.
doi:10.1021/la105067x
PMCID: PMC3128200  PMID: 21322612
13.  Expression, purification and preliminary X-ray diffraction studies of the transcriptional factor PyrR from Bacillus halodurans  
The gene-regulation factor PyrR from B. halodurans has been crystallized in two crystal forms. Preliminary crystallographic analysis showed that the protein forms tetramers in both space groups.
The PyrR transcriptional regulator is widely distributed in bacteria. This RNA-binding protein is involved in the control of genes involved in pyrimidine biosynthesis, in which uridyl and guanyl nucleotides function as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of two crystal forms of Bacillus halodurans PyrR are reported. One of the forms belongs to the monoclinic space group P21 with unit-cell parameters a = 59.7, b = 87.4, c = 72.1 Å, β = 104.4°, while the other form belongs to the orthorhombic space group P22121 with unit-cell parameters a = 72.7, b = 95.9, c = 177.1 Å. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of four and six monomers per asymmetric unit; a crystallographic tetramer is formed in both forms.
doi:10.1107/S1744309108018307
PMCID: PMC2494968  PMID: 18678934
Bacillus halodurans; pyrimidine biosynthesis; riboswitch-like element; PyrR; transcriptional/translational factor
14.  Expression, purification, crystallization and preliminary X-ray diffraction analysis of α-11 giardin from Giardia lamblia  
α-11 giardin from the intestinal protozoan parasite, G. lamblia has been cloned, expressed, purified and crystallized under two different conditions and in two different space groups. Crystals from the first condition diffracted to 1.1 Å and belong to a primitive orthorhombic space group and crystals obtained in the second condition diffracted to 2.93 Å and belong to a primitive monoclinic space group.
α-11 Giardin, a protein from the annexin superfamily, is a 35.0 kDa protein from the intestinal protozoan parasite Giardia lamblia which triggers a form of diarrhea called giardiasis. Here, the cloning, expression, purification and the crystallization of α-11 giardin under two different conditions and in two different space groups is reported. Crystals from the first condition diffracted to 1.1 Å and belong to a primitive orthorhombic space group, while crystals from the second condition, which included calcium in the crystallization solution, diffracted to 2.93 Å and belong to a primitive monoclinic space group. Determination of the detailed atomic structure of α-11 giardin will provide a better insight into its biological function and might establish whether this class of proteins is a potential drug target against giardiasis.
doi:10.1107/S1744309106039650
PMCID: PMC2225204  PMID: 17077490
α-11 giardin; annexins; Giardia lamblia
15.  Structure of recombinant Leishmania donovani pteridine reductase reveals a disordered active site 
The structure of L. donovani pteridine reductase has been targeted to assist in a program of structure-based inhibitor research. Crystals that diffracted to 2.5 Å resolution were obtained and the structure has been solved. Unfortunately, the active site is disordered and this crystal form is unsuitable for use in characterizing enzyme–ligand interactions.
Pteridine reductase (PTR1) is a potential target for drug development against parasitic Trypanosoma and Leishmania species, protozoa that are responsible for a range of serious diseases found in tropical and subtropical parts of the world. As part of a structure-based approach to inhibitor development, specifically targeting Leishmania species, well ordered crystals of L. donovani PTR1 were sought to support the characterization of complexes formed with inhibitors. An efficient system for recombinant protein production was prepared and the enzyme was purified and crystallized in an orthorhombic form with ammonium sulfate as the precipitant. Diffraction data were measured to 2.5 Å resolution and the structure was solved by molecular replacement. However, a sulfate occupies a phosphate-binding site used by NADPH and occludes cofactor binding. The nicotinamide moiety is a critical component of the active site and without it this part of the structure is disordered. The crystal form obtained under these conditions is therefore unsuitable for the characterization of inhibitor complexes.
doi:10.1107/S174430911004724X
PMCID: PMC3079966  PMID: 21206018
antifolates; pteridine reductase; Leishmania; pterins; Trypanosoma
16.  Purification, crystallization and preliminary crystallographic studies of a Kunitz-type proteinase inhibitor from tamarind (Tamarindus indica) seeds 
A 21 kDa Kunitz-type proteinase inhibitor was purified from tamarind (T. indica) seeds, crystallized and characterized by X-ray diffraction.
A Kunitz-type proteinase inhibitor has been purified from tamarind (Tamarindus indica) seeds. SDS–PAGE analysis of a purified sample showed a homogeneous band corresponding to a molecular weight of 21 kDa. The protein was identified as a Kunitz-type proteinase inhibitor based on N-terminal amino-acid sequence analysis. It was crystallized by the vapour-diffusion method using PEG 6000. The crystals belonged to the orthorhombic space group C2221, with unit-cell parameters a = 37.2, b = 77.1, c = 129.1 Å. Diffraction data were collected to a resolution of 2.7 Å. Preliminary crystallographic analysis indicated the presence of one proteinase inhibitor molecule in the asymmetric unit, with a solvent content of 44%.
doi:10.1107/S1744309109023495
PMCID: PMC2705649  PMID: 19574654
Kunitz-type proteinase inhibitors; Tamarindus indica
17.  Crystallization of a 79 kDa fragment of the hook protein FlgE from Campylobacter jejuni  
A 79 kDa fragment of FlgE from C. jejuni has been crystallized.
A 79 kDa fragment of the bacterial flagellar hook protein FlgE from Campylobacter jejuni was cloned, overexpressed, purified and crystallized. Two different crystal forms were obtained. Synchrotron X-ray diffraction data showed that the first crystal form, which diffracted to 4.9 Å resolution, belonged to the tetragonal crystal system, with space group I4122 and unit-cell parameters a = b = 186.2, c = 386.6 Å, α = β = γ = 90°. The second crystal form diffracted to 2.5 Å resolution and belonged to the monoclinic crystal system, with space group P21 and unit-cell parameters a = 75.7, b = 173.8, c = 150.8 Å, α = γ = 90, β = 106.5°. SeMet protein was also overexpressed, purified and crystallized, and a 2.6 Å resolution MAD data set was collected.
doi:10.1107/S1744309111043272
PMCID: PMC3232163  PMID: 22139190
FlgE; hook proteins; bacterial flagella; motility; universal joints; nanomachines
18.  X-ray crystallographic studies on C-phycocyanins from cyanobacteria from different habitats: marine and freshwater 
The protein C-phycocyanin, involved in photosynthesis, has been purified from three cyanobacterial species: Spirulina, Phormidium and Lyngbya. These three proteins have been crystallized and characterized using X-ray crystallography.
C-phycocyanins from three cyanobacterial cultures of freshwater and marine habitat, Spirulina, Phormidium and Lyngbya spp., were purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. Blue-coloured crystals in different crystal forms, monoclinic and hexagonal, were obtained for the three species. The crystals took 1–12 weeks to grow to full size using polyethylene glycols of different molecular weights as precipitants. The amino-acid sequences of these proteins show high similarity to other known C-­phycocyanins from related organisms; however, the C-­phycocyanins reported here showed different biochemical and biophysical properties, i.e. molecular weight, stability etc. The X-ray diffraction data were collected at resolutions of 3.0 Å for the monoclinic and 3.2 and 3.6 Å for the hexagonal forms. The unit-cell parameters corresponding to the monoclinic space group P21 are a = 107.33, b = 115.64, c = 183.26 Å, β = 90.03° for Spirulina sp. C-­phycocyanin and are similar for crystals of Phormidium and Lyngbya spp. C-­phycocyanins. Crystals belonging to the hexagonal space group P63, with unit-cell parameters a = b = 154.97, c = 40.35 Å and a = b = 151.96, c = 39.06 Å, were also obtained for the C-phycocyanins from Spirulina and Lyngbya spp., respectively. The estimated solvent content is around 50% for the monoclinic crystals of all three species assuming the presence of two hexamers per asymmetric unit. The solvent content is 66.5 and 64.1% for the hexagonal crystals of C-phycocyanin from Spirulina and Lyngbya spp. assuming the presence of one αβ monomer per asymmetric unit.
doi:10.1107/S1744309105025649
PMCID: PMC1978106  PMID: 16511175
cyanobacteria; C-phycocyanin
19.  Crystallization and preliminary X-ray analysis of βC–S lyases from two oral streptococci 
The βC-S lyases from two oral bacteria, Streptococcus anginosus and S. gordonii, were cloned, overproduced, purified and crystallized. The obtained crystals were characterized by X-ray diffraction.
Hydrogen sulfide, which causes oral malodour, is generally produced from l-­cysteine by the action of βC–S lyase from oral bacteria. The βC–S lyases from two oral bacteria, Streptococcus anginosus and S. gordonii, have been cloned, overproduced, purified and crystallized. X-ray diffraction data were collected from the two types of crystals using synchrotron radiation. The crystal of S. anginosus βC–S lyase belonged to the orthorhombic space group P212121, with unit-cell parameters a = 67.0, b = 111.1, c = 216.4 Å, and the crystal of S. gordonii βC–S lyase belonged to the same space group, with unit-cell parameters a = 58.0, b = 73.9. c = 187.6 Å. The structures of the βC–S lyases were solved by molecular-replacement techniques.
doi:10.1107/S1744309109030371
PMCID: PMC2795589  PMID: 19724121
βC–S lyases; Streptococcus anginosus; Streptococcus gordonii
20.  Crystallization of recombinant bifunctional nuclease TBN1 from tomato 
Glycosylated recombinant bifunctional nuclease from tomato has been crystallized and preliminary X-ray diffraction analysis was performed.
The endonuclease TBN1 from Solanum lycopersicum (tomato) was expressed in Nicotiana benthamiana leaves and purified with suitable quality and in suitable quantities for crystallization experiments. Two crystal forms (orthorhombic and rhombohedral) were obtained and X-ray diffraction experiments were performed. The presence of natively bound Zn2+ ions was confirmed by X-ray fluorescence and by an absorption-edge scan. X-ray diffraction data were collected from the orthorhombic (resolution of 5.2 Å) and rhombohedral (best resolution of 3.2 Å) crystal forms. SAD, MAD and MR methods were applied for solution of the phase problem, with partial success. TBN1 contains three Zn2+ ions in a similar spatial arrangement to that observed in nuclease P1 from Penicillium citrinum.
doi:10.1107/S1744309110048177
PMCID: PMC3079990  PMID: 21206042
plant endonucleases; cancer; antitumour activity; MAD
21.  Redetermination of tantalum penta­bromide, (TaBr5)2  
Crystals of di-μ-bromido-bis­[tetra­bromidotantalum(V)], (TaBr5)2, were obtained by recrystallization at 773 K. A first crystal structure study of (TaBr5)2 was reported by Rolsten [J. Am. Chem. Soc. (1958) ▶, 80, 2952–2953], who analysed the powder diffraction pattern and came to the conclusion that it crystallizes isotypically with (NbBr5)2 in a primitive ortho­rhom­bic cell. These findings are not in agreement with our current results of a monoclinic C-centred structure. (TaBr5)2 is isotypic with α-(NbCl5)2. The crystal structure contains [TaBr6] octa­hedra sharing common edges forming [TaBr5]2 dimers. Two crystallographically independent dimers with symmetries m and 2/m and Ta⋯Ta distances of 4.1574 (11) and 4.1551 (15) Å, respectively, are present in the structure.
doi:10.1107/S1600536810032538
PMCID: PMC3007875  PMID: 21588474
22.  Crystallization and preliminary crystallographic analysis of cgHle, a homoserine acetyltransferase homologue, from Corynebacterium glutamicum  
The enzyme cgHle from C. glutamicum, which has acetyl ester hydrolase activity, was crystallized in four different crystal forms. X-ray diffraction data have been collected to a resolution of 1.2 Å.
CgHle is an enzyme that is encoded by gene cg0961 from Corynebacterium glutamicum. The physiological function of cgHle is so far unclear. Bioinformatic annotations based on sequence homology indicated that cgHle may be an acetyl-CoA:homoserine acetyl transferase and as such may be involved in methionine biosynthesis, but recent evidence has shown that it is an esterase that catalyzes the hydrolysis of acetyl esters. Here, the crystallization of cgHle in two orthorhombic crystal forms, a trigonal crystal form and a monoclinic crystal form is described. The trigonal crystals have a solvent content of 83.7%, which is one of the highest solvent contents ever found for protein crystals. One of the orthorhombic crystals diffracted X-rays to at least 1.2 Å resolution.
doi:10.1107/S1744309108039146
PMCID: PMC2628851  PMID: 19153452
CgHle; Corynebacterium glutamicum; homoserine acetyltransferases
23.  On the Mechanism of Crystalline Polymorph Selection by Polymer Heteronuclei 
The phase-selective crystallization of acetaminophen (ACM) using insoluble polymers as heteronuclei was investigated in a combined experimental and computational effort to elucidate the mechanism of polymer-induced heteronucleation (PIHn). ACM heteronucleates from supersaturated aqueous solution in its most thermodynamically stable monoclinic form on poly(n-butyl methacrylate), whereas the metastable orthorhombic form is observed on poly(methyl methacrylate). When ACM crystals were grown through vapor deposition, only the monoclinic polymorph was observed on each polymer. Each crystallization condition leads to a unique powder X-ray diffraction pattern with the major preferred orientation corresponding to the crystallographic faces in which these crystal phases nucleate from surfaces of the polymers. The molecular recognition events leading to these outcomes are elucidated with the aid of computed polymer-crystal binding energies using docking simulations. This investigation illuminates the mechanism by which phase-selection occurs during the crystallization of ACM using polymers as heteronuclei paving the way for the improvement of methods for polymorph selection and discovery based on heterogeneous nucleation promoters.
doi:10.1021/la200689a
PMCID: PMC3124555  PMID: 21591791
crystal polymorphism; X-ray diffractometry; preferred orientation; molecular dynamics; binding energy
24.  Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method 
A high-resolution structure of human triosephosphate isomerase was obtained from crystals improved by means of the gel-tube method.
Crystals of human triosephosphate isomerase with two crystal morphologies were obtained using the normal vapour-diffusion technique with identical crystallization conditions. One had a disordered plate shape and the crystals were hollow (crystal form 1). As a result, this form was very fragile, diffracted to 2.8 Å resolution and had similar crystallographic parameters to those of the structure in the Protein Data Bank. The other had a fine needle shape (crystal form 2) and was formed more abundantly than crystal form 1, but was unsuitable for structure analysis. Since the normal vapour-diffusion method could not control the crystal morphology, gel-tube methods, both on earth and under microgravity, were applied for crystallization in order to control and improve the crystal quality. Whereas crystal form 1 was only slightly improved using this method, crystal form 2 was greatly improved and diffracted to 2.2 Å resolution. Crystal form 2 contained a homodimer in the asymmetric unit, which was biologically essential. Its overall structure was similar to that of except for the flexible loop, which was located at the active centre Lys13.
doi:10.1107/S1744309105008341
PMCID: PMC1952429  PMID: 16511037
microgravity; triosephosphate isomerase; gel; counter-diffusion technique
25.  A case of structure determination using pseudosymmetry 
When properly applied, pseudosymmetry can be used to improve crystallographic phases through averaging and to facilitate crystal structure determination.
Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P21212. Surprisingly, crystals of the inactive C94A mutant of Mac-1 displayed monoclinic symmetry with space group P21, despite the use of native orthorhombic Mac-1 microcrystals for seeding. Attempts to solve the structure of the C94A mutant by MAD phasing in the monoclinic space group did not produce an interpretable map. The native Patterson map of the C94A mutant showed two strong peaks along the (1 0 1) diagonal, indicating possible translational pseudosymmetry in space group P21. Interestingly, one-third of the monoclinic reflections obeyed pseudo-orthorhombic P21212 symmetry similar to that of the wild-type crystals and could be indexed and processed in this space group. The pseudo-orthorhombic and monoclinic unit cells were related by the following vector operations: a m = b o − c o, b m = a o and c m = −2c o − b o. The pseudo-orthorhombic subset of data produced good SAD phases, leading to structure determination with one monomer in the asymmetric unit. Subsequently, the structure of the Mac-1 mutant in the monoclinic form was determined by molecular replacement, which showed six molecules forming three translationally related dimers aligned along the (1 0 1) diagonal. Knowing the geometric relationship between the pseudo-orthorhombic and the monoclinic unit cells, all six molecules can be generated in the monoclinic unit cell directly without the use of molecular replacement. The current case provides a successful example of the use of pseudosymmetry as a powerful phase-averaging method for structure determination by anomalous diffraction techniques. In particular, a structure can be solved in a higher pseudosymmetry subcell in which an NCS operator becomes a crystallographic operator. The geometrical relationships between the subcell and parental cell can be used to generate a complete molecular representation of the parental asymmetric unit for refinement.
doi:10.1107/S0907444909039912
PMCID: PMC2789005  PMID: 19966420
pseudosymmetry; structure determination; cysteine proteases; Mac-1

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