Unit Cell Parametersa Research Articles

Bianchiniite, Ba2(Ti4+V3+)(As2O5)2OF, a new diarsenite mineral from the Monte Arsiccio mine, Apuan Alps, Tuscany, Italy

AbstractThe new mineral bianchiniite, Ba2(Ti4+V3+)(As2O5)2OF, has been discovered in the Monte Arsiccio mine, Apuan Alps, Tuscany, Italy. It occurs as brown {001} tabular crystals, up to 1 mm across, with a vitreous lustre. It is brittle, with a perfect {001} cleavage. Streak is brownish. In reflected light, bianchiniite is grey, with orange–yellow internal reflections. It is weakly bireflectant, with a very weak anisotropy in shades of grey. Minimum and maximum reflectance data for COM wavelengths [Rmin/Rmax(%), (λ, nm)] are: 5.0/5.8 (470), 5.7/6.5 (546), 5.7/7.0 (589) and 5.2/6.3 (650). Electron microprobe analyses gave (wt.% – average of 10 spot analyses): TiO210.34, V2O33.77, Fe2O33.76, As2O344.36, Sb2O30.22, SrO 0.45, BaO 34.79, PbO 0.28, F 1.77, sum 99.74, –O = F –0.75, total 98.99. On the basis of 12 anions per formula unit, the empirical formula of bianchiniite is (Ba2.00Sr0.04Pb0.02)Σ2.06(Ti4+1.14V3+0.44Fe3+0.42)Σ2.00[(As3.96Sb0.02)Σ3.98O10](O1.18F0.82)Σ2.00. Bianchiniite is tetragonal, space groupI4/mcm, with unit-cell parametersa= 8.7266(4),c= 15.6777(7) Å,V= 1193.91(12) Å3andZ= 8. Its crystal structure was refined from single-crystal X-ray diffraction data toR1= 0.0134 on the basis of 555 unique reflections withFo> 4σ(Fo) and 34 refined parameters. The crystal structure shows columns of corner-sharing [Ti/(V,Fe)]-centred octahedra running alongc, connected alongaandbthrough (As2O5) dimers. A {001} layer of Ba-centred [10+2]-coordinated polyhedra is intercalated between (As2O5) dimers. Bianchiniite has structural relations with fresnoite- and melilite-group minerals. The name honours the two mineral collectors Andrea Bianchini (b. 1959) and Mario Bianchini (b. 1962) for their contribution to the knowledge of the mineralogy of pyrite ± baryte ± iron-oxide ore deposits from the Apuan Alps.

Bosoite, a new silica clathrate mineral from Chiba Prefecture, Japan

AbstractBosoite (IMA2014-023) is a new silica clathrate mineral containing hydrocarbon molecules in its crystal structure. Bosoite can be considered structurally as a silica analogue of the structure-H gas hydrate, where guest molecules are trapped in cage-like voids constructed of the host framework. The mineral occurs in the Miocene tuffaceous sedimentary rocks at Arakawa, Minami-boso City, Chiba Prefecture, Japan. Bosoite is hexagonal, and it crystallises as an epitaxial intergrowth on chibaite crystals, with the {0001} of bosoite parallel to octahedral {111} form of chibaite. Crystals are colourless and transparent with vitreous lustre. The calculated density is 2.04 g/cm3. The empirical formula (based on 2 O apfu and guest molecules assumed as CH4) is Na0.01(Si0.98Al0.02)Σ1.00O2⋅0.50CH4; the end-member formula is SiO2⋅nCxH2x+2. Bosoite has the space groupP6/mmm, with the unit-cell parametersa= 13.9020(3) Å,c= 11.2802(2) Å,V= 1887.99(6) Å3andZ= 34. The crystal structure of bosoite was refined by single-crystal X-ray diffraction and converged toR1= 4.26% for the average model andR1= 2.96% for the model where all oxygen sites are split.

Chitoporin from Serratia marcescens: recombinant expression, purification and crystallization.

Serratia marcescens is an opportunistic pathogen that commonly causes hospital-acquired infections and can utilize chitin-enriched nutrients as an alternative energy source. This study reports the identification of a chitoporin (ChiP), termed SmChiP, from the outer membrane of S. marcescens. Sequence alignment with genetically characterized ChiPs suggests that SmChiP is more closely related to the monomeric EcChiP from Escherichia coli than to the trimeric VhChiP from Vibrio campbellii. A single crystal of SmChiP grown under the condition 22%(w/v) PEG 8000, 0.1 M calcium acetate, 0.1 M MES pH 6.0 diffracted X-ray synchrotron radiation to 1.85 Å resolution. SmChiP co-crystallized with chitohexaose under the condition 19%(w/v) PEG 1500, 2 M ammonium phosphate monobasic, 0.1 M HEPES pH 7.0 diffracted X-rays to 2.70 Å resolution. Preliminary crystallographic analysis shows that both SmChiP crystal forms contain one molecule per asymmetric unit and that they belong to the tetragonal space groups P42212 and P41212, respectively. The SmChiP crystal has unit-cell parameters a = 82.97, b = 82.97, c = 189.53 Å, α = β = γ = 90°, while the crystal of SmChiP in complex with chitohexaose has unit-cell parameters a=73.24, b = 73.24, c = 213.46 Å, α = β = γ = 90°. Initial assessment of the complex structure clearly revealed electron density for the sugar ligand. Structure determination of SmChiP in the absence and presence of chitohexaose should reveal the molecular basis of chitin utilization by S. marcescens.

The structure of kaliophilite KAlSiO4, a long-lasting crystallographic problem.

Kaliophilite is a feldspathoid mineral found in two Italian magmatic provinces and represents one of the 12 known phases with composition close to KAlSiO4. Despite its apparently simple formula, the structure of this mineral revealed extremely complex and resisted structure solution for more than a century. Samples from the Vesuvius-Monte Somma and Alban Hills volcanic areas were analyzed through a multi-technique approach, and finally the crystal structure of kaliophilite was solved using 3D electron diffraction and refined against X-ray diffraction data of a twinned crystal. Results were also ascertained by the Rietveld method using synchrotron powder intensities. It was found that kaliophilite crystallizes in space group P3 with unit-cell parameters a = 27.0597 (16), c = 8.5587 (6) Å, V = 5427.3 (7) Å3 and Z = 54. The kaliophilite framework is a variant of the tridymite topology, with alternating SiO4 and AlO4 tetrahedra forming sheets of six-membered rings (63 nets), which are connected along [001] by sharing the apical oxygen atoms. Considering the up (U) and down (D) orientations of the linking vertex, kaliophilite is the first framework that contains three different ring topologies: nine (1-3-5) (UDUDUD) rings, six (1-2-3) (UUUDDD) rings and twelve (1-2-4) (UUDUDD) rings. This results in a relatively open (19.9 tetrahedra nm-3) channel system with multiple connections between the double six-ring cavities. Such a framework requires a surprisingly large unit cell, 27 times larger than the cell of kalsilite, the simplest phase with the same composition. The occurrence of some Na for K substitution (3-10%) may be related to the characteristic structural features of kaliophilite. Micro-twinning, pseudo-symmetries and anisotropic hkl-dependent peak broadening were also detected, and they may account for the elusive character of the kaliophilite crystal structure.

The coiled-coil domain of glycosomal membrane-associated Leishmania donovani PEX14: cloning, overexpression, purification and preliminary crystallographic analysis.

The glycosomal membrane-associated Leishmania donovani protein PEX14, which plays a crucial role in protein import from the cytosol to the glycosomal matrix, consists of three domains: an N-terminal domain where the signalling molecule binds, a transmembrane domain and an 84-residue coiled-coil domain (CC) that is responsible for oligomerization. CCs are versatile domains that participate in a variety of functions including supramolecular assembly, cellular signalling and transport. Recombinant PEX14 CC was cloned, overexpressed, affinity-purified with in-column thrombin cleavage and further purified by size-exclusion chromatography. Crystals that diffracted to 1.98 Å resolution were obtained from a condition consisting of 1.4 M sodium citrate tribasic dihydrate, 0.1 M HEPES buffer pH 7.5. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a=143.98, b = 32.62, c = 95.62 Å, β = 94.68°. Structure determination and characterization are in progress.

The crystal structure of alstonite, BaCa(CO3)2: an extraordinary example of ‘hidden’ complex twinning in large single crystals

AbstractAlstonite, BaCa(CO3)2, is a mineral described almost two centuries ago. It is widespread in Nature and forms magnificent cm-sized crystals. Notwithstanding, its crystal structure was still unknown. Here, we report the crystal-structure determination of the mineral and discuss it in relationship to other polymorphs of BaCa(CO3)2. Alstonite is trigonal, space groupP31m, with unit-cell parametersa= 17.4360(6),c= 6.1295(2) Å,V= 1613.80(9) Å3andZ= 12. The crystal structure was solved and refined toR1= 0.0727 on the basis of 4515 reflections withFo> 4σ(Fo) and 195 refined parameters. Alstonite is formed by the alternation, alongc, of Ba-dominant and Ca-dominant layers, separated by CO3groups parallel to {0001}. The main take-home message is to show that not all structure determinations of minerals/compounds can be solved routinely. Some crystals, even large ones displaying excellent diffraction quality, can be twinned in complex ways, thus making their study a crystallographic challenge.

Crystal structure of the catalytic subunit of bovine pyruvate dehydrogenase phosphatase.

Mammalian pyruvate dehydrogenase (PDH) activity is tightly regulated by phosphorylation and dephosphorylation, which is catalyzed by PDH kinase isomers and PDH phosphatase isomers, respectively. PDH phosphatase isomer 1 (PDP1) is a heterodimer consisting of a catalytic subunit (PDP1c) and a regulatory subunit (PDP1r). Here, the crystal structure of bovine PDP1c determined at 2.1 Å resolution is reported. The crystals belonged to space group P3221, with unit-cell parameters a = b = 75.3, c = 173.2 Å. The structure was solved by molecular-replacement methods and refined to a final R factor of 21.9% (Rfree = 24.7%). The final model consists of 402 of a possible 467 amino-acid residues of the PDP1c monomer, two Mn2+ ions in the active site, an additional Mn2+ ion coordinated by His410 and His414, two MnSO4 ion pairs at special positions near the crystallographic twofold symmetry axis and 226 water molecules. Several new features of the PDP1c structure are revealed. The requirements are described and plausible bases are deduced for the interaction of PDP1c with PDP1r and other components of the pyruvate dehydrogenase complex.

Isselite, Cu6(SO4)(OH)10(H2O)4⋅H2O, a new mineral species from Eastern Liguria, Italy

AbstractThe new mineral isselite, Cu6(SO4)(OH)10(H2O)4⋅H2O, has been discovered in the Lagoscuro mine, Monte Ramazzo mining complex, Genoa, Eastern Liguria, Italy. It occurs as sprays of blue acicular crystals, up to 0.1 mm long, associated with brochantite and posnjakite. Streak is light blue and the lustre is vitreous. Isselite is brittle, with irregular fracture and good cleavage on {001} and {100}. Measured density is 3.00(2) g/cm3. Isselite is optically biaxial (–), with α = 1.599(2), β = 1.633(2) and γ = 1.647(2) (determined in white light). The measured 2V is 63.6(5)°. Dispersion is moderate, withr>v. The optical orientation isX=b,Y=candZ=a. Isselite is pleochroic, withX= light blue,Y= blue,Z= blue;X<<Z<Y. Electron microprobe analyses give (wt.%): SO311.45(21), MgO 0.31(7), CoO 1.07(14), NiO 9.41(90), CuO 51.29(126), ZnO 1.10(20), H2Ocalc24.21, total 98.84. The empirical formula of isselite, based on Σ(Mg,Co,Ni,Cu,Zn) = 6 atoms per formula unit, is (Cu4.80Ni0.94Co0.11Zn0.10Mg0.06)Σ6.00(S1.06O4.19)(OH)10⋅5H2O. Isselite is orthorhombic, space groupPmn21, with unit-cell parametersa= 6.8070(14),b= 5.8970(12),c= 20.653(4) Å,V= 829.0(3) Å3andZ= 2. The crystal structure of isselite was refined from single-crystal X-ray diffraction data toR1= 0.067 on the basis of 2964 reflections withFo> 4σ(Fo). It shows a layered structure formed by zig-zag {001} layers of Cu-centred polyhedra. Sulfate groups occur in the interlayer along with one H2O group. Isselite is chemically related to redgillite and montetrisaite.

A commensurately modulated crystal structure and the physical properties of a novel polymorph of the caesium manganese phosphate CsMnPO4.

A novel modification of the CsMnPO4 β-phase was achieved by hydrothermal synthesis at 553 K. The compound crystallizes in the monoclinic system with the basic unit-cell parameters a = 11.0699 (4), b = 11.0819 (6), c = 9.1106 (3) Å, γ = 119.480 (5)o; the modulation vectors are q1 = 0.4a* and q2 = 0.4b*. The structure was determined based on single-crystal X-ray diffraction data obtained from a pseudo-merohedral twin using a superspace approach in the (3 + 2)D symmetry group P11a(a1,b1,0)0(a2,b2,0)0 and refined to R = 0.083 for 10 266 reflections with I > 3σ(I). It is considered as a low-temperature polymorph of CsMnPO4 with the same UUUDDD-type layer topology built by MnO4 and PO4 tetrahedra, and stacked in a framework in the same manner as β-tridymite. Large open channels parallel to the [110] and [001] directions incorporate Cs atoms. All Cs atoms are distributed along the asuper = 55.35 (1) and bsuper = 55.41 (1) axes of the large unit cell with pseudo periods of asuper/5 and bsuper/5 which are broken mainly by the positions of oxygen atoms (orientation of Mn- and P-centered tetrahedra). The β-phase is discussed as a member of the morphotropic series of manganese phosphates with large cations of AMnPO4, where A = Cs, Rb, K and Ag. The title compound is an antiferromagnet with the Neel temperature TN = 4.5 K.

Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant.

The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 Å) were obtained and diffracted to 3.0 Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli (PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 Å resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipoamide succinyltransferase isolated without an expression tag and in this novel crystal form.

Levantite, KCa3(Al2Si3)O11(PO4), a new latiumite-group mineral from the pyrometamorphic rocks of the Hatrurim Basin, Negev Desert, Israel

AbstractLevantite, with the end-member formula KCa3(Al2Si3)O11(PO4), is the phosphate analogue of latiumite, KCa3(Al3Si2)O11(SO4, CO3) found in gehlenite–wollastonite hornfels on Har Parsa, Negev Desert, Israel. Levantite forms later zones on long-prismatic crystals of latiumite. Rarer homogeneous colourless levantite crystals up to 0.2 mm long and with mean composition (K0.94Ba0.01Na0.01□0.04)Σ1.00(Ca2.96Mg0.03)Σ2.99{(Si2.69Al2.06Fe3+0.16P0.06)Σ4.97O11}[(PO4)0.65(SO4)0.35]Σ1.00were noted. Minerals of the levantite–latiumite series are associated with gehlenite, wollastonite, clinopyroxene of the esseneite–diopside series, anorthite and Ti-bearing andradite. Levantite crystalises in space groupP21with unit-cell parametersa= 12.1006(9) Å,b= 5.1103(4) Å,c= 10.8252(9) Å, β = 107.237(8)°,V= 639.34(9) Å3andZ= 2. The structure of levantite is analogous to latiumite. It is formed by tetrahedral hybridzweierdouble layers [(Si,Al)10O22] connected by Ca atoms. Three Ca atoms linked to different double layers are bridged over by (PO4) and minor (SO4) groups. K atoms reside in the cavities between two superimposedzweierdouble layers. The measured micro-indentation hardness of levantite gave VHN50= 580(19) (mean of 14), range 550–611 kg/mm2, which correlates with 5 on the Mohs scale. Cleavage is good on (100). Twinning on (100) is polysynthetic or simple. The calculated density is 2.957 g cm–3. Levantite is optically negative with α = 1.608(2), β = 1.618(2), γ = 1.622(2) (λ = 589 nm), 2Vmeas.= 70(5)° and 2Vcalc.= 64.3°. Dispersion of the optical axes r > v is weak; the optical orientation is:Z=b,X^c= 22–27°; and it is non-pleochroic. Minerals of the levantite–latiumite series from Israel show characteristic Raman spectra with the main bands at 994 cm–1[ν1(SO4)2–] and 945 cm–1[ν1(PO4)3–]. The band intensity ν1(PO4)3–/ν1(SO4) ratio is well correlated with P and S contents in the investigated minerals. The strongest lines in the powder diffraction pattern [dobs, Å (I, %) (hkl)] are: 3.0762(100)(310), 2.8551(96)($\bar 2$13), 2.9704(92)($\bar 3$12), 2.8573(83)(013), 2.5552(66)(020), 2.8228(48)(212), 2.8893(40)(400), and 3.0634(30)(103).

X-ray crystallographic analysis of the catalytic domain of α-1,3-glucanase FH1 from Paenibacillus glycanilyticus overexpressed in Brevibacillus choshinensis.

α-1,3-Glucanase hydrolyzes α-1,3-glucan, an insoluble linear α-1,3-linked homopolymer of glucose that is found in the extracellular polysaccharides produced by oral streptococci in dental plaque and in fungal cell walls. This enzyme could be of application in dental care and the development of fungal cell-wall lytic enzymes, but its three-dimensional structure has not been available to date. In this study, the recombinant catalytic domain of α-1,3-glucanase FH1 from Paenibacillus glycanilyticus FH11, which is classified into glycoside hydrolase family 87, was prepared using a Brevibacillus choshinensis expression system and purified in a soluble form. Crystals of the purified protein were produced by the sitting-drop vapor-diffusion method. Diffraction data were collected to a resolution of 1.6 Å using synchrotron radiation. The crystals obtained belonged to the tetragonal space group P41212 or P43212, with unit-cell parameters a=b=132.6, c = 76.1 Å. The space group and unit-cell parameters suggest that there is one molecule in the asymmetric unit.

Crystal structure of the ternary semiconductor Cu2In14/3□4/3Se8determined by X-ray powder diffraction data

The crystal structure of the partially ordered vacancy compound Cu2In14/3□4/3Se8, belonging to the system I3-III7-□2-VI12, was analyzed using X-ray powder diffraction data. Several structural models were derived from the structure of the selenium-rich phaseβ-Cu0.39In1.2Se2by permuting the cations in the available Wyckoff positions. The refinement of the best model by the Rietveld method in the tetragonal space groupP$\overline 4 $2c(No 112), with unit-cell parametersa= 5.7487(3) Å,c= 11.5106(6) Å,V= 380.40(3) Å3, led toRp= 9.0%,Rwp= 9.9%,Rexp= 7.2%,S= 1.4 for 134 independent reflections. This model has the following Wyckoff site atomic distribution: Cu in 2e(0,0,0); In in 2b(½,0,¼), 2d(0,½,¼), and 2f(½,½,0);□ in 2f(½,½,0); Se in 8n(x,y,z).

Crystallization and X-ray analysis of all of the players in the autoregulation of the ataRT toxin-antitoxin system.

The ataRT operon from enteropathogenic Escherichia coli encodes a toxin-antitoxin (TA) module with a recently discovered novel toxin activity. This new type II TA module targets translation initiation for cell-growth arrest. Virtually nothing is known regarding the molecular mechanisms of neutralization, toxin catalytic action or translation autoregulation. Here, the production, biochemical analysis and crystallization of the intrinsically disordered antitoxin AtaR, the toxin AtaT, the AtaR-AtaT complex and the complex of AtaR-AtaT with a double-stranded DNA fragment of the operator region of the promoter are reported. Because they contain large regions that are intrinsically disordered, TA antitoxins are notoriously difficult to crystallize. AtaR forms a homodimer in solution and crystallizes in space group P6122, with unit-cell parameters a=b=56.3, c = 160.8 Å. The crystals are likely to contain an AtaR monomer in the asymmetric unit and diffracted to 3.8 Å resolution. The Y144F catalytic mutant of AtaT (AtaTY144F) bound to the cofactor acetyl coenzyme A (AcCoA) and the C-terminal neutralization domain of AtaR (AtaR44-86) were also crystallized. The crystals of the AtaTY144F-AcCoA complex diffracted to 2.5 Å resolution and the crystals of AtaR44-86 diffracted to 2.2 Å resolution. Analysis of these structures should reveal the full scope of the neutralization of the toxin AtaT by AtaR. The crystals belonged to space groups P6522 and P3121, with unit-cell parameters a = b = 58.1, c = 216.7 Å and a = b = 87.6, c=125.5 Å, respectively. The AtaR-AtaT-DNA complex contains a 22 bp DNA duplex that was optimized to obtain high-resolution data based on the sequence of two inverted repeats detected in the operator region. It crystallizes in space group C2221, with unit-cell parameters a = 75.6, b = 87.9, c = 190.5 Å. These crystals diffracted to 3.5 Å resolution.

PicW2 from Picea wilsonii: preparation, purification, crystallization and X-ray diffraction analysis.

Low temperature is a major limiting factor for plant growth and development. Dehydrin proteins are generally induced in response to low-temperature stress. In previous research, a full-length dehydrin gene, PicW2, was isolated from Picea wilsonii and its expression was associated with hardiness to cold. In order to gain insight into the mechanism of low-temperature tolerance by studying its three-dimensional crystal structure, prokaryotically expressed PicW2 dehydrin protein was purified using chitosan-affinity chromatography and gel filtration, and crystallized using the vapour-diffusion method. The crystal grew in a condition consisting of 0.1 M HEPES pH 8.0, 25%(w/v) PEG 3350 using 4 mg ml-1 protein solution at 289 K. X-ray diffraction data were collected from a crystal at 100 K to 2.82 Å resolution. The crystal belonged to space group C121, with unit-cell parameters a = 121.55, b = 33.26, c = 73.39 Å, α = γ = 90.00, β= 109.01°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.87 Å3 Da-1 and a solvent content of 57.20%. Owing to a lack of structures of homologous dehydrin proteins, molecular-replacement trials failed. Data collection for selenium derivatization of PicW2 and crystal structure determination is currently in progress.

Crystal structure of Escherichia coli purine nucleoside phosphorylase in complex with 7-deazahypoxanthine.

Purine nucleoside phosphorylases (EC 2.4.2.1; PNPs) reversibly catalyze the phosphorolytic cleavage of glycosidic bonds in purine nucleosides to generate ribose 1-phosphate and a free purine base, and are key enzymes in the salvage pathway of purine biosynthesis. They also catalyze the transfer of pentosyl groups between purine bases (the transglycosylation reaction) and are widely used for the synthesis of biologically important analogues of natural nucleosides, including a number of anticancer and antiviral drugs. Potent inhibitors of PNPs are used in chemotherapeutic applications. The detailed study of the binding of purine bases and their derivatives in the active site of PNPs is of particular interest in order to understand the mechanism of enzyme action and for the development of new enzyme inhibitors. Here, it is shown that 7-deazahypoxanthine (7DHX) is a noncompetitive inhibitor of the phosphorolysis of inosine by recombinant Escherichia coli PNP (EcPNP) with an inhibition constant Ki of 0.13 mM. A crystal of EcPNP in complex with 7DHX was obtained in microgravity by the counter-diffusion technique and the three-dimensional structure of the EcPNP-7DHX complex was solved by molecular replacement at 2.51 Å resolution using an X-ray data set collected at the SPring-8 synchrotron-radiation facility, Japan. The crystals belonged to space group P6122, with unit-cell parameters a = b = 120.370, c = 238.971 Å, and contained three subunits of the hexameric enzyme molecule in the asymmetric unit. The 7DHX molecule was located with full occupancy in the active site of each of the three crystallographically independent enzyme subunits. The position of 7DHX overlapped with the positions occupied by purine bases in similar PNP complexes. However, the orientation of the 7DHX molecule differs from those of other bases: it is rotated by ∼180° relative to other bases. The peculiarities of the arrangement of 7DHX in the EcPNP active site are discussed.

Graftonite-(Mn), ideallyM1MnM2,M3Fe2(PO4)2, and graftonite-(Ca), ideallyM1CaM2,M3Fe2(PO4)2, two new minerals of the graftonite group from Poland

AbstractTwo new minerals of the graftonite group, graftonite-(Mn), ideallyM(1)MnM(2),M(3)Fe2(PO4)2, and graftonite-(Ca), ideallyM(1)CaM(2),M(3)Fe2(PO4)2, were discovered in phosphate nodules of two beryl–columbite–phosphate pegmatites at Lutomia and Michałkowa, respectively, in the Góry Sowie Block, Lower Silesia, southwest Poland. Graftonite-(Mn) is pinkish brown, whereas graftonite-(Ca) shows more brownish colouration. Both minerals have a vitreous lustre, a good cleavage observed along (010) and irregular fracture; both are transparent and neither of them is fluorescent. They are brittle and have a Mohs hardness of ~5. The minerals are non-pleochroic, colourless in all orientations, biaxial (+), with mean refractive indices α = 1.710(2) and 1.690(2), β = 1.713(2) and 1.692(2), and γ = 1.725(2) and 1.710(5), respectively. With complete order of Ca at theM(1) site, the formulae of the holotype crystals areM(1)(Mn0.70Ca0.30)M(2),M(3)(Fe1.34Mn0.60Mg0.06Zn0.01)Σ3(PO4)2for graftonite-(Mn) andM(1)(Ca0.98Mn0.02)M(2),M(3)(Fe1.38Mn0.56Mg0.05)Σ3(PO4)2for graftonite-(Ca). Both crystal chemistry and crystal-structure refinement (R1= 2.34 and 1.63%, respectively) indicate that theM(1) site is occupied dominantly by Mn in graftonite-(Mn) and by Ca in graftonite-(Ca), and theM(2) andM(3) sites are occupied by Fe2+and Mn2+, with Fe2+dominant over Mn2+at the aggregateM(2) +M(3) sites. Graftonite-(Mn) and graftonite-(Ca) are isostructural with graftonite,M(1)FeM(2),M(3)Fe2(PO4)2(monoclinic system; space-group symmetryP21/c), with the unit-cell parametersa= 8.811(2) Å,b= 11.494(2) Å,c= 6.138(1) Å, β = 99.23(3)° and V = 613.5(4) Å3, anda= 8.792(2) Å,b= 11.743(2) Å,c= 6.169(1) Å, β = 99.35(3)° andV= 628.5(1) Å3, respectively. The densities calculated on the basis of molar weights and unit-cell volumes are 3.793 g/cm3for graftonite-(Mn) and 3.592 g/cm3for graftonite-(Ca). The eight strongest lines in powder X-ray diffraction patterns on the basis of single-crystal data are, respectively [d, Å,I(hkl)]: 2.874, 100, (230 + 040); 2.858, 79, (221); 3.506, 73, (130); 2.717, 79, ($\bar{3}$11); 2.952, 55, (131); 2.916, 53, ($\bar{1}$12); 2.899, 44, (300); 3.016, 35, ($\bar{1}$02); and 3.654, 100, (130); 2.979, 85, (221); 3.014, 77, (230); 3.042, 76, (040 +$\bar{1}$12); 2.834, 68, ($\bar{3}$11); 3.097, 57, (131); 3.133, 56, ($\bar{1}$02); 2.542, 30, (311). Both minerals are common primary phosphates in phosphate nodules, occurring as lamellar intergrowths with sarcopside ± triphylite/lithiophilite, products of exsolution from a (Li,Ca)-rich graftonite-like parent phase crystallized at high temperature from P-bearing hydrosaline melts.

Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding.

The structure of orthorhombic lysozyme has been obtained at 298 K and pH 4.5 using sodium chloride as the precipitant and in the presence of sodium phosphate at a concentration as low as 5 mM. Crystals belonging to space group P212121 (unit-cell parameters a = 30, b = 56, c = 73 Å, α = β = γ = 90.00°) diffracted to a resolution higher than 1 Å, and the high quality of these crystals permitted the identification of a phosphate ion bound to Arg14 and His15. The binding of this ion produces long-range conformational changes affecting the loop containing Ser60-Asn74. The negatively charged phosphate ion shields the electrostatic repulsion of the positively charged arginine and histidine residues, resulting in higher stability of the phosphate-bound lysozyme. Additionally, a low-humidity orthorhombic variant was obtained at pH 4.5, and comparison with those previously obtained at pH 6.5 and 9.5 shows a 1.5 Å displacement of the fifth α-helix towards the active-site cavity, which might be relevant to protein function. Since lysozyme is broadly used as a model protein in studies related to protein crystallization and amyloid formation, these results indicate that the interaction of some anions must be considered when analysing experiments performed at acidic pH values.

The putative siderophore-interacting protein from Vibrio anguillarum: protein production, analysis, crystallization and X-ray crystallographic studies.

Siderophore-interacting proteins (SIPs) play an important role in iron acquisition in many bacteria. SIPs release iron from the internalized ferric siderophore complex by reducing ferric iron to ferrous iron, but how the iron is reduced is not well understood. Here, a sip gene was identified in the genome of Vibrio anguillarum 775. To further understand the catalytic mechanism of the protein, the SIP was overexpressed in Escherichia coli Rosetta (DE3) cells, purified and crystallized for X-ray diffraction analysis. The crystal diffracted to 1.113 Å resolution and belonged to space group P21, with unit-cell parameters a= 64.63, b = 58.47, c = 70.65 Å, β = 114.19°.

The crystal structure of the lipoaminopeptaibol helioferin, an antibiotic peptide from Mycogone rosea.

The crystal structure of the natural nonapeptide antibiotic helioferin has been determined and refined to 0.9 Å resolution. Helioferin consists of helioferin A and B, which contain 2-(2'-aminopropyl)aminoethanol (Apae) and 2-[(2'-aminopropyl)methylamino]ethanol (Amae) at their respective alkanolamine termini. In addition, helioferin contains the unusual amino-acid residues α-aminoisobutyric acid (Aib) and (2S,4S,6S)-2-amino-6-hydroxy-4-methyl-8-oxodecanoic acid (Ahmod). The amino-terminus is capped with 2-methyl-n-1-octanoic acid (M8a). The peptide crystallizes with a 1:1 molar ratio of helioferin A and B in the monoclinic space group C2, with unit-cell parameters a = 34.711, b = 10.886, c = 17.150 Å, β = 93.05°. The peptide backbone folds in a regular right-handed α-helical conformation, with eight intramolecular hydrogen bonds, all but one forming 5→1 interactions. The two aliphatic chains of the fatty-acyl (M8a) and the second residue (Ahmod) extend out of the α-helical structure in opposite directions and lead to a corkscrew-like shape of the peptide molecule. Halogen anions (Cl- and F-) have been co-crystallized with the peptide molecules, implying a positive charge at the aminoalcohol end of the peptide. In the tightly packed crystal the helices are linked head to tail via the anions by electrostatic, hydrogen-bond and van der Waals interactions, forming continuous helical rods. Two nonparallel rods (forming an angle of 118°) interact directly via hydrogen bonds and via the anions, forming a double layer. Successive double layers are held together only via van der Waals contacts. The helical axes of successive double layers are also related by an angle of 118°. The structure of helioferin reported here and the previously determined structure of the homologous leucinostatin A have a total straight length of about 21 Å, indicating a different membrane-modifying bioactivity from that of long-chain, amphiphilic peptaibols.