D. rostrata lectin was crystallized by hanging-drop vapor diffusion. The crystal belongs to the orthorhombic space group I222 and diffracted to 1.87 Å resolution.
Lectins from the Diocleinae subtribe (Leguminosae) are highly similar proteins that promote various biological activities with distinctly differing potencies. The structural basis for this experimental data is not yet fully understood. Dioclea rostrata lectin was purified and crystallized by hanging-drop vapour diffusion at 293 K. The crystal belongs to the orthorhombic space group I222, with unit-cell parameters a = 61.51, b = 88.22, c = 87.76 Å. Assuming the presence of one monomer per asymmetric unit, the solvent content was estimated to be about 47.9%. A complete data set was collected at 1.87 Å resolution.
lectins; Dioclea rostrata
A lectin from C. maritima was crystallized using the vapour-diffusion method and crystals diffracted to 2.1 Å resolution. A molecular-replacement search found a solution with a correlation coefficient of 69.2% and an R factor of 42.5%, refinement is in progress.
A lectin from Canavalia maritima seeds (ConM) was purified and submitted to crystallization experiments. The best crystals were obtained using the vapour-diffusion method at a constant temperature of 293 K and grew in 7 d. A complete structural data set was collected to 2.1 Å resolution using a synchrotron-radiation source. The ConM crystal belongs to the orthorhombic space group P21212, with unit-cell parameters a = 67.15, b = 70.90, c = 97.37 Å. A molecular-replacement search found a solution with a correlation coefficient of 69.2% and an R factor of 42.5%. Crystallographic refinement is under way.
lectins; Canavalia maritima
Tyrosyl-tRNA synthetase from the hyperthermophilic archaeon A. pernix K1 was cloned, purified and crystallized. The crystals belonged to the tetragonal space group P43212, with unit-cell parameters a = b = 66.1, c = 196.2 Å, and diffracted to beyond 2.15 Å resolution at 100 K.
Hyperthermophilic archaeal tyrosyl-tRNA synthetase from Aeropyrum pernix K1 was cloned and overexpressed in Escherichia coli. The expressed protein was purified by Cibacron Blue affinity chromatography following heat treatment at 363 K. Crystals suitable for X-ray diffraction studies were obtained under optimized crystallization conditions in the presence of 1.5 M ammonium sulfate using the hanging-drop vapour-diffusion method. The crystals belonged to the tetragonal space group P43212, with unit-cell parameters a = b = 66.1, c = 196.2 Å, and diffracted to beyond 2.15 Å resolution at 100 K.
aminoacyl-tRNA synthetase; tyrosine tRNA; Aeropyrum pernix K1
Industrially used carbohydrate oxidase was successfully crystallized in several forms, diffraction data suitable for structural analysis were collected.
Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized. The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions. Several different crystal forms were obtained using the hanging-drop vapour-diffusion method, two of which were used for diffraction measurements. Hexagon-shaped crystals (form I) diffracted to 2.66 Å resolution, with unit-cell parameters a = b = 55.7, c = 610.4 Å and apparent space group P6222. Analysis of the data quality showed almost perfect twinning of the crystals. Attempts to solve the structure by molecular replacement did not give satisfactory results. Recently, clusters of rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to the monoclinic system C2, with unit-cell parameters a = 132.9, b = 56.6, c = 86.5 Å, β = 95.7°. Data sets were collected to a resolution of 2.4 Å. The structure was solved by the molecular-replacement method. Model refinement is currently in progress.
carbohydrate oxidases; Microdochium nivale
Recombinant β-glucosidase from wheat seedlings complexed with a substrate aglycone has been crystallized in a hexameric active form. A diffraction data set has been collected at 1.7 Å.
The wheat β-glucosidase TaGlu1b, which is only active in a hexameric form, was tagged with 6×His at the N-terminus, overexpressed in Escherichia coli and purified in two steps. The protein complexed with a substrate aglycone was crystallized at 293 K from a solution containing 10 mM HEPES pH 7.2, 1 M LiSO4 and 150 mM NaCl using the hanging-drop vapour-diffusion method. Diffraction data were collected to 1.7 Å at the Photon Factory. The crystal belongs to space group P4132, with unit-cell parameters a = b = c = 194.65 Å, α = β = γ = 90°. The asymmetric unit was confirmed by molecular-replacement solution to contain one monomer, giving a solvent content of 72.1%.
β-glucosidases; DIMBOA; hexamers; wheat
α-Enolase from human liver (hENO1) was expressed as a soluble protein and purified by affinity column chromatography and gel filtration. Crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.5 Å resolution.
Enolase is a multifunctional enzyme that plays important roles in many biological and disease processes. α-Enolase from human liver (hENO1) was expressed as a soluble protein and purified by affinity column chromatography and gel filtration. Crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.5 Å resolution. The crystals belonged to space group P21, with unit-cell parameters a = 72.85, b = 66.02, c = 79.43 Å, β = 94.54°.
human liver α-enolase
The crystallization and preliminary X-ray diffraction analysis of a red marine alga lectin isolated from H. musciformis is reported.
HML, a lectin from the red marine alga Hypnea musciformis, defines a novel lectin family. Orthorhombic crystals of HML belonging to space group P212121 grew within three weeks at 293 K using the hanging-drop vapour-diffusion method. A complete data set was collected at 2.4 Å resolution. HML is the first marine alga lectin to be crystallized.
red marine algal lectin; Hypnea musciformis; novel lectin family
The bifunctional enzyme catalase-phenol oxidase from S. thermophilum was crystallized by the hanging-drop vapour-diffusion method in space group P21 and diffraction data were collected to 2.8 Å resolution.
Catalase-phenol oxidase from Scytalidium thermophilum is a bifunctional enzyme: its major activity is the catalase-mediated decomposition of hydrogen peroxide, but it also catalyzes phenol oxidation. To understand the structural basis of this dual functionality, the enzyme, which has been shown to be a tetramer in solution, has been purified by anion-exchange and gel-filtration chromatography and has been crystallized using the hanging-drop vapour-diffusion technique. Streak-seeding was used to obtain larger crystals suitable for X-ray analysis. Diffraction data were collected to 2.8 Å resolution at the Daresbury Synchrotron Radiation Source. The crystals belonged to space group P21 and contained one tetramer per asymmetric unit.
Scytalidium thermophilum; Humicola insolens; catalases; phenol oxidases; catechol oxidases; CATPO
The α-2,6-sialyltransferase PM0188 from P. multocida was purified using affinity-column chromatographic methods and crystallized using the hanging-drop vapour-diffusion method at 293 K.
Sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine-5-monophospho-N-acetylneuraminic acid (CMP-NeuAc) to the carbohydrate group of various glycoproteins. These glycoproteins are involved in inflammation, embryogenesis, immune defence and metastasis of cancer cells by cell–cell interactions or cell–matrix interactions. The α-2,6-sialyltransferase PM0188 from Pasteurella multocida was purified using affinity-column chromatographic methods and crystallized using the hanging-drop vapour-diffusion method at 293 K. MAD data were collected to 1.9 Å resolution from an SeMet-substituted crystal. The crystal belongs to space group P21, with unit-cell parameters a = 52.9, b = 61.0, c = 64.6 Å, α = γ = 90, β = 112.3°. Assuming the presence of one molecule in the asymmetric unit, the solvent content is estimated to be about 45%.
The flavin-dependent monooxygenase RebC has been crystallized by the hanging-drop vapour-diffusion method and initial X-ray diffraction analysis has been completed.
The flavin-dependent monooxygenase RebC is a key enzyme in the biosynthesis of the indolocarbazole rebeccamycin. The synthesis of rebeccamycin is of great interest as it has been shown to be a natural antitumour agent. The enzyme has been recombinantly expressed in Escherichia coli and purified to homogeneity. Hanging-drop vapour diffusion in combination with microseeding was used to obtain suitable crystals for X-ray diffraction. Data were collected to 2.4 Å; the crystals belonged to space group P21, with unit-cell parameters a = 63.08, b = 77.85, c = 63.94 Å, α = γ = 90, β = 108.11°.
RebC; indolocarbazole; FAD-dependent monooxygenases
Sagitoxin, a novel cardiotoxin from the venom of Naja naja saggitifera, has been successfully isolated, purified to homogeneity and crystallized.
Sagitoxin, a novel cardiotoxin from the venom of Naja naja saggitifera, has been successfully isolated, purified to homogeneity and crystallized. The toxin was purified using successive separation steps on a CM-Sephadex C-50 column and a reverse-phase column. The 6.75 kDa toxin was sequenced by the Edman method using a PPSQ-21 protein sequencer. It was crystallized using the hanging-drop vapour-diffusion method. The hexagonal-shaped crystals diffracted to 3.0 Å resolution and belonged to space group P64, with unit-cell parameters a = b = 111.1, c = 137.3 Å, γ = 120°. There are 36 molecules in the unit cell, which has an approximate solvent content of 80%. Structure determination revealed that the molecules of sagitoxin associate in a hexameric form and create a pore in the centre which has functional significance.
cardiotoxins; sagitoxin; toxins
Crystals of 6-aminohexanoate-oligomer hydrolase have been obtained by the sitting-drop vapour-diffusion method using sodium citrate as a precipitant. Diffraction data for native and K2PtCl4-derivative crystals were collected to resolutions of 2.00 and 2.20 Å, respectively.
6-Aminohexanoate-oligomer hydrolase (NylC) from Agromyces sp. KY5R was expressed in Escherichia coli JM109 and purified by ammonium sulfate fractionation, anion-exchange column chromatography and gel-filtration chromatography. NylC was crystallized by the sitting-drop vapour-diffusion method with sodium citrate as a precipitant in 0.1 M HEPES buffer pH 7.5 containing 0.2 M NaCl. Diffraction data were collected from native and K2PtCl4-derivative crystals to resolutions of 2.00 and 2.20 Å, respectively. The obtained crystal was plate-shaped, with an I-centred orthorhombic space group and unit-cell parameters a = 155.86, b = 214.45, c = 478.80 Å. The anomalous difference Patterson map of the K2PtCl4-derivative crystal suggested that the space group was I222 rather than I212121.
6-aminohexanoate-oligomer hydrolase; Agromyces sp. KY5R
The substrate binding protein (SP_0149) of an ABC transporter from Streptococcus pneumoniae was molecularly cloned, overexpressed and purified. Diffraction quality crystals were grown using the hanging-drop vapour-diffusion technique.
A truncated (29 residues from the N-terminus) and N-terminal His-tagged form of SP_0149 from pneumococcal strain ATCC BAA-334 was overexpressed and purified to homogeneity using affinity and gel-filtration chromatography. Diffraction quality crystals were grown at 293 K using the hanging-drop vapour-diffusion technique. X-ray diffraction data were collected to 2.3 Å resolution from a single-crystal that belonged to the orthorhombic space group P212121 with the unit-cell parameters a = 54.56, b = 75.61, c = 75.52 Å. The calculated values of the Matthews coefficient assuming one molecule (with calculated molecular weight of 30 400 Da) in the crystal asymmetric unit and the corresponding solvent content were 2.56 Å3 Da−1 and 52.0%, respectively.
ABC transporter; Streptococcus pneumoniae; SP_0149; ATCC BAA-334
Crystals of the carbohydrate-recognition domain of human langerin were obtained that diffracted synchrotron radiation to 1.5 Å resolution.
Langerin, a lectin that is specific to Langerhans cells, interacts with glycoconjugates through its carbohydrate-recognition domain (CRD). This carbohydrate binding occurs by an avidity-based mechanism that is enabled by the neck domain responsible for trimerization. Langerin binds HIV through its CRD and thus plays a protective role against its propagation by the internalization of virions in Birbeck granules. Here, the overproduction, purification and crystallization of the langerin CRD is reported. Crystals obtained by the hanging-drop vapour-diffusion method allowed the collection of a complete data set to 1.5 Å resolution and belonged to the tetragonal space group P42, with unit-cell parameters a = b = 79.55, c = 90.14 Å.
langerin; carbohydrate-recognition domains; lectins; Strep-Tag II; Birbeck granules; HIV; host–pathogen interactions
The hatching enzyme of zebrafish, ZHE1, was expressed, purified and crystallized using the hanging-drop vapour-diffusion method. The crystal belonged to space group P212121 and diffracted X-rays to a resolution of 1.14 Å.
The hatching enzyme of the zebrafish, ZHE1 (29.3 kDa), is a zinc metalloprotease that catalyzes digestion of the egg envelope (chorion). ZHE1 was heterologously expressed in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant. Two diffraction data sets with resolution ranges 50.0–1.80 and 50.0–1.14 Å were independently collected from two crystals and were merged to give a highly complete data set over the full resolution range 50.0–1.14 Å. The space group was assigned as primitive orthorhombic P212121, with unit-cell parameters a = 32.9, b = 62.5, c = 87.4 Å. The crystal contained one ZHE1 molecule in the asymmetric unit.
ZHE1; hatching enzymes; zebrafish
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.
scaffolding protein; bacteriophage ϕ29
The CRD domain of GRP from H. sapiens has been expressed, purified and crystallized and X-ray diffraction data have been collected to a resolution of 2.0 Å.
Galectins are a family of animal lectins which share similar carbohydrate-recognition domains (CRDs) and an affinity for β-galactosides. A novel human galectin-related protein named GRP (galectin-related protein; previously known as HSPC159) comprises only one conserved CRD with 38 additional N-terminal residues. The C-terminal fragment of human GRP (GRP-C; residues 38–172) containing the CRD has been expressed and purified. The protein was crystallized using the hanging-drop vapour-diffusion method from a solution containing 2% PEG 400 and 2M ammonium sulfate in 100 mM Tris–HCl buffer pH 7.5. Diffraction data were collected to a resolution limit of 2.0 Å at beamline 3W1A of Beijing Synchrotron Radiation Facility at 100 K. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 123.07, b = 96.67, c = 61.56 Å, β = 118.72°. The estimated Matthews coefficient was 2.6 Å3 Da−1, corresponding to 51.8% solvent content.
galectins; carbohydrate-recognition domains; galectin-related protein
Raucaffricine glucosidase, an enzyme involved in the biosynthesis of monoterpenoid indole alkaloids in the plant Rauvolfia serpentina, was crystallized by the hanging-drop vapour-diffusion method using PEG4000 as precipitant. The crystals diffract to 2.3 Å resolution and belong to space group I222.
Raucaffricine glucosidase (RG) is an enzyme that is specifically involved in the biosynthesis of indole alkaloids from the plant Rauvolfia serpentina. After heterologous expression in Escherichia coli cells, crystals of RG were obtained by the hanging-drop vapour-diffusion technique at 293 K with 0.3 M ammonium sulfate, 0.1 M sodium acetate pH 4.6 buffer and 11% PEG 4000 as precipitant. Crystals belong to space group I222 and diffract to 2.30 Å, with unit-cell parameters a = 102.8, b = 127.3, c = 215.8 Å.
raucaffricine glucosidase; indole alkaloid metabolism; biosynthesis; Rauvolfia serpentina
Rice lectin was crystallized and analyzed by X-ray crystallography.
Lectins with sugar-binding specificity are widely distributed in higher plants and various other species. The expression of rice lectin from Oryza sativa is up-regulated in the growing coleoptile when anaerobic stress persists. A rice lectin of molecular weight 15.2 kDa has been crystallized using the hanging-drop vapour-diffusion method. From the diffraction of the lectin crystals at 1.93 Å resolution, the unit cell belongs to space group P31, with unit-cell parameters a = 98.58, b = 98.58, c = 44.72 Å. Preliminary analysis indicates that there are two lectin molecules in an asymmetric unit with a large solvent content, 70.1%.
Mhp1, a hydantoin transporter from M. liquefaciens, was purified and crystallized. Diffraction data were collected to 2.85 Å resolution; the crystal belonged to the orthorhombic space group P212121.
The integral membrane protein Mhp1 from Microbacterium liquefaciens transports hydantoins and belongs to the nucleobase:cation symporter 1 family. Mhp1 was successfully purified and crystallized. Initial crystals were obtained using the hanging-drop vapour-diffusion method but diffracted poorly. Optimization of the crystallization conditions resulted in the generation of orthorhombic crystals (space group P212121, unit-cell parameters a = 79.7, b = 101.1, c = 113.8 Å). A complete data set has been collected from a single crystal to a resolution of 2.85 Å with 64 741 independent observations (94% complete) and an R
merge of 0.12. Further experimental phasing methods are under way.
transporters; nucleobase:cation symporter 1 family; membrane proteins; hydantoins
The ligand-binding domain of metabotropic glutamate receptor 7 has been overexpressed, purified, and crystallized by the hanging-drop vapour-diffusion method. A complete data set has been collected to 3.30 Å.
Glutamate is the major excitatory neurotransmitter and its metabotropic glutamate receptor (mGluR) plays an important role in the central nervous system. The ligand-binding domain (LBD) of mGluR subtype 7 (mGluR7) was produced using the baculovirus expression system and purified from the culture medium. The purified protein was characterized by gel-filtration chromatography, SDS–PAGE and a ligand-binding assay. Crystals of mGluR7 LBD were grown at 293 K by the hanging-drop vapour-diffusion method. The crystals diffracted X-rays to 3.30 Å resolution using synchrotron radiation and belong to the trigonal space group P3121, with unit-cell parameters a = b = 92.4, c = 114.3 Å. Assuming the presence of one protomer per crystallographic asymmetric unit, the Matthews coefficient V
M was calculated to be 2.5 Å3 Da−1 and the solvent content was 51%.
metabotropic glutamate receptors; ligand-binding domains
NAD+-preferring aldohexose dehydrogenase from the thermoacidophilic archaeon T. acidophilum was crystallized using the hanging-drop vapour-diffusion technique and X-ray diffraction data were collected to a resolution of 2.8 Å.
The aldohexose dehydrogenase from the thermoacidophilic archaeon Thermoplasma acidophilum (AldT) is a 28 kDa molecular-weight enzyme that catalyzes the oxidation of various aldohexoses, with a preference for NAD+ rather than NADP+ as a cofactor. The recombinant AldT was crystallized using the hanging-drop vapour-diffusion technique at 293 K under several acidic conditions with polyethylene glycol (PEG) and ammonium sulfate as precipitants. Optimization of the initial crystallizations conditions yielded single crystals in solution containing 0.1 M sodium acetate pH 4.6, 18%(w/v) PEG 4000, 0.2 M ammonium sulfate and 15%(v/v) glycerol. An X-ray diffraction data set was collected to a resolution of 2.8 Å.
aldohexose dehydrogenase; glucose dehydrogenase; d-mannose; short-chain dehydrogenase/reductase (SDR) family; Thermoplasma acidophilum
Human S100A13 protein was cloned, expressed, purified and crystallized by the hanging-drop vapour-diffusion method. The crystals obtained belonged to space group P212121 and diffracted to a resolution of 1.8 Å.
S100A13 is a member of the S100 family of EF-hand-containing calcium-binding proteins and plays an important role in the secretion of fibroblast growth factor-1 and interleukin 1α, two pro-angiogenic factors released by the endoplasmic reticulum/Golgi-independent non-classical secretory pathway. Human S100A13 was heterologously expressed in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant. The crystals diffracted X-rays from a synchrotron-radiation source to 1.8 Å resolution and the space group was assigned as primitive orthorhombic P212121.
S100A13; EF-hand calcium-binding proteins
Reducing-end-xylose releasing exo-oligoxylanase (Rex) from B. halodurans C-125 was crystallized. A diffraction data set was collected to 1.35 Å resolution.
The reducing-end xylose-releasing exo-oligoxylanase (Rex) from Bacillus halodurans C-125, a novel family GH8 glycoside hydrolase, was crystallized by the hanging-drop vapour-diffusion method using 13.6 mg ml−1 purified Rex, 5.6%(v/v) polyethylene glycol 4000, 70 mM sodium acetate pH 4.6 and 30%(v/v) glycerol. Suitable crystals grew after incubation for 5 d at 293 K. The crystals belonged to space group P212121, with unit-cell parameters a = 52.69, b = 86.02, c = 87.92 Å. X-ray diffraction data were collected at a resolution of 1.35 Å.
reducing-end xylose-releasing exo-oligoxylanase; glycoside hydrolases
A sulfotransferase from M. tuberculosis was crystallized and preliminarily analyzed using X-ray diffraction.
Sulfotransferase STF1 from the Mycobacterium tuberculosis H37Rv genome was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals diffract to 1.5 Å resolution using synchrotron radiation at SPring-8. The crystals are monoclinic and belong to space group P21, with unit-cell parameters a = 40.86, b = 95.76, c = 48.04 Å, β = 106.43°. The calculated Matthews coefficient is approximately 2.1 Å3 Da−1 assuming the presence of one molecule of STF1 in the asymmetric unit. A substrate-binding assay using a PAP–agarose column suggests that STF1 exhibits sulfotransferase activity.
sulfotransferase; Mycobacterium tuberculosis