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1.
Two different heparin-binding fragments of human fibronectin have been crystallized in forms which are suitable for crystal structure analyses. The 30 kDa hep-2A fragment, consisting of type III domains 12–14, was crystallized from solutions containing ammonium sulfate or polyethylene glycol 6000. The crystals grown in ammonium sulfate solutions were orthorhombic with space group I222 or I212121 with a = 68.1 Å, b = 88.6 Å, and c = 144.9 Å. The crystals grown in polyethylene glycol solutions are hexagonal with space group P6122 or P6522 witha a = b = 66.7 Å and c = 245.7 Å. The 40 kDa hep-2B fragment, consisting of type III domains 12–15, was also crystallized from solutions containing ammonium sulfate with the addition of glycerol. Glycerol proved an effective agent for reducing the number of crystals in the crystallization experiments, and thus, increasing the size of the crystals in these experiments. This crystal form is nearly isomorphous to the orthorhombic form of the hep-2A fragment with space group I222 or I212121 and a = 67.5 Å, b = 87.0 Å, and c = 144.3 Å. All crystal forms diffract to at least 3.5 Å resolution and contain a single molecule in the asymmetric unit. © 1993 Wiley-Liss, Inc.  相似文献   

2.
Escherichia coli BamB is the largest of four lipoproteins in the β-barrel assembly machinery (BAM) complex. It interacts with the periplasmic domain of BamA, an integral outer membrane protein (OMP) essential for OMP biogenesis. Although BamB is not essential, it serves an important function in the BAM complex, significantly increasing the folding efficiency of some OMPs in vivo and in vitro. To learn more about the BAM complex, we solved structures of BamB in three different crystal forms. BamB crystallized in space groups P213, I222, and P212121, with one molecule per asymmetric unit in each case. Crystals from the space group I222 diffracted to 1. 65-Å resolution. BamB forms an eight-bladed β-propeller with a central pore and is shaped like a doughnut. A DALI search revealed that BamB shares structural homology to several eukaryotic proteins containing WD40 repeat domains, which commonly have β-propeller folds and often serve as scaffolding proteins within larger multi-protein complexes that carry out signal transduction, cell division, and chemotaxis. Using mutagenesis data from previous studies, we docked BamB onto a BamA structural model and assessed known and possible interactions between these two proteins. Our data suggest that BamB serves as a scaffolding protein within the BAM complex by optimally orienting the flexible periplasmic domain of BamA for interaction with other BAM components and chaperones. This may facilitate integration of newly synthesized OMPs into the outer membrane.  相似文献   

3.
The three-dimensional crystal structure of the DNA/RNA nonspecific endonuclease from Serratia marcescenswas refined at the resolution of 1.07 Å to Rfactor of 12.4% and R freefactor of 15.3% using the anisotropic approximation. The structure includes 3924 non-hydrogen atoms, 715 protein-bound water molecules, and a Mg2+ion in each binding site of each subunit of the nuclease homodimeric globular molecule. The 3D topological model of the enzyme was revealed, the inner symmetry of the monomers in its N-and C-termini was found, and the local environment of the magnesium cofactor in the nuclease active site was defined. Mg2+ion was found to be bound to the Asn119 residue and surrounded by five associated water molecules that form an octahedral configuration. The coordination distances for the water molecules and the O1atom of Asn119 were shown to be within the range of 2.01–2.11 Å. The thermal factors for the magnesium ion in subunits are 7.08 and 4.60 Å2, and the average thermal factors for the surrounding water molecules are 11.14 and 10.30 Å2, respectively. The region of the nuclease subunit interactions was localized, and the alternative side chain conformations were defined for 51 amino acid residues of the nuclease dimer.  相似文献   

4.
Voltage‐dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high‐resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell‐free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad‐range screening using a bicelle crystallization method produced crystals in space groups C222 and P22121, which diffracted to a resolution of 3.10 and 3.15 Å, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P22121 were oriented anti‐parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with β‐strands, hydrophilic interactions with loop regions, and protein–lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo‐ or hetero‐oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis‐regulating proteins in the Bcl‐2 family.  相似文献   

5.
Concanavalin A (Con A) is the best-known plant lectin and has importantin vitrobiological activities arising from its specific saccharide-binding ability. Its exact biological role still remains unknown. The complexes of Con A with 4′-nitro-phenyl-α-d-mannopyranoside (α-PNM) and 4′-nitrophenyl-α-d-glucopyranoside (α-PNG) have been crystallized in space group P21212 with cell dimensionsa= 135.19 Å,b= 155.38 Å,c= 71.25 Å anda= 134.66 Å,b= 155.67 Å, andc= 71.42 Å, respectively. X-ray diffraction intensities to 2.75 Å for the α-PNM and to 3.0 Å resolution for the α-PNG complex have been collected. The structures of the complexes were solved by molecular replacement and refined by simulated annealing methods to crystallographic R-factor values of 0.185/0.186 and free-R-factor values of 0.260/0.274, respectively. In both structures, the asymmetric unit contains four molecules arranged as a tetramer, with approximate 222 symmetry. A saccharide molecule is bound in the sugar-binding site near the surface of each monomer. The nonsugar (aglycon) portion of the compounds used helps to identify the exact orientation of the saccharide in the sugar-binding pocket and is involved in major interactions between tetramers. The hydrogen bonding network in the region of the binding site has been analyzed, and only minor differences with the previously reported Con A–methyl-α-d-mannopyranoside complex structure have been observed. Structural differences that may contribute to the slight preference of the lectin for mannosides over glucosides are discussed. Calculations indicate a negative electrostatic surface potential for the saccharide binding site of Con A, which may be important for its biological activity. It is also shown in detail how a particular class of hydrophobic ligands interact with one of the three so-called characteristic hydrophobic sites of the lectins.  相似文献   

6.
The crystal structure of cyclo(Pro-Gly)3 (PG3) complex with LiSCN (C22H30N7O6SLi) has been solved by x-ray diffraction. The crystals belong to the space group R3 in the hexagonal setting with unit cell parameters of a = 12.581(1), c = 29.705(3) Å, V = 4072.0 Å3, Z = 6, Mr = 527.53, Dc = 1.23 g/cm3. The crystal structure was solved by direct methods using the program SHELXS-86 and refined to an R value of 5.3% for 1645 reflections (I > 2σI). There are two conformers in the crystal structure. One conformer has three carbonyls on one side and three on the other side of the peptide plane. The other conformer has all six of the carbonyls on the same side of the peptide plane. Both of these conformers bind independently to a Li ion. Based on the conformers of the Li complex and other reported ion complexes formed by PG3, we propose a model for the transport of ions across the lipid membrane. The features of the model are as follows: (1) PG3 forms a hexameric stack in a lipid bilayer when complexing and transporting metal ions. (2) It undergoes a conformational flipping in order pass the ion along the channel. The energy required for the conformational change involved in the flipping of the PG3 molecule may be provided by the applied potential during ion transport. © 1994 John Wiley & Sons, Inc.  相似文献   

7.
Formylmethanofuran:tetrahydromethanopterin formyltransferase from the hyperthermophilic methanogenic Archaeon Methanopyrus kandleri (growth temperature optimum 98°C) was crystallized by vapor diffusion methods. Crystal form M obtained with 2-methyl-2,4-pentanediol as precipitant displayed the space group P21 with unit cell parameters of a = 87.0 Å, b = 75.4 Å, c = 104.7 Å, and β = 113.9° and diffracted better than 2 Å resolution. Crystal form P grown from polyethylene glycol 8000 belonged to the space group I4122 and had unit cell parameters of 157.5 Å and 242.1 Å. Diffraction data to 1.73 Å were recorded. Crystal form S which was crystallized from (NH4)2SO4in the space group I4122 with unit cell parameters of 151.3 Å and 249.5 Å diffracted at least to 2.2 Å resolution. All crystal forms probably have four molecules per asymmetric unit and are suitable for X-ray structure analysis. © 1996 Wiley-Liss, Inc.  相似文献   

8.
The crystal structures of the nucleotide-empty (AE), 5′-adenylyl-β,γ-imidodiphosphate (APNP)-bound, and ADP (ADP)-bound forms of the catalytic A subunit of the energy producer A1AO ATP synthase from Pyrococcus horikoshii OT3 have been solved at 2.47 Å and 2.4 Å resolutions. The structures provide novel features of nucleotide binding and depict the residues involved in the catalysis of the A subunit. In the AE form, the phosphate analog SO42− binds, via a water molecule, to the phosphate binding loop (P-loop) residue Ser238, which is also involved in the phosphate binding of ADP and 5′-adenylyl-β,γ-imidodiphosphate. Together with amino acids Gly234 and Phe236, the serine residue stabilizes the arched P-loop conformation of subunit A, as shown by the 2.4-Å structure of the mutant protein S238A in which the P-loop flips into a relaxed state, comparable to the one in catalytic β subunits of F1FO ATP synthases. Superposition of the existing P-loop structures of ATPases emphasizes the unique P-loop in subunit A, which is also discussed in the light of an evolutionary P-loop switch in related A1AO ATP synthases, F1FO ATP synthases, and vacuolar ATPases and implicates diverse catalytic mechanisms inside these biological motors.  相似文献   

9.
The structure of the N,N-dimethylthioformamide (DMTF) solvated gallium(III) ion has been determined in solution by means of extended X-ray absorption fine structure (EXAFS) spectroscopy. The gallium(III) ion is four-coordinate in tetrahedral fashion with a mean Ga-S bond distance of 2.233(2) Å in DMTF solution. At the dissolution of indium(III) perchlorate or trifluoromethanesulfonate in DMTF coordinated solvent molecules are partly reduced to sulfide ions, and a tetrameric complex with the composition [In4S4(SHN(CH3)2)12]4+ is formed. The structure of the solid tetrameric complex in the perchlorate salt was solved with single crystal X-ray diffraction. Four indium(III) ions and four sulfide ions form a highly symmetric heterocubane structure where each indium binds three bridging sulfide ions and each sulfide ion binds three indium(III) ions with a mean In-S bond distance of 2.584(1) Å, and S-In-S angles of 90.3(1)°. Each indium(III) additionally binds three DMTF molecules at significantly longer mean In-S bond distance, 2.703(1) Å; the S-In-S angles are in the range 80.3-90.4°. Large angle X-ray scattering data on a DMTF solution of indium(III) trifluoromethanesulfonate show that the same tetrameric species characterized in the solid state is also present in solution, whereas the EXAFS measurements only give information about the In-S bond distances due to the short core hole lifetime.  相似文献   

10.
The present study explored regulation of electrogenic ion transport across cultured mouse endometrial epithelium by extracellular ATP using the short-circuit current (I SC ) and the patch-clamp techniques. The cultured endometrial monolayers responded to apical application of ATP with an increase in I SC in a concentration-dependent manner (EC50 at 3 μm). Replacement of Cl in the bathing solution or treatment of the cells with Cl channel blockers, DIDS and DPC, markedly reduced the I SC , indicating that a substantial portion of the ATP-activated I SC was Cl-dependent. Amiloride at a concentration (10 μm) known to block Na+ channels was found to have no effect on the ATP-activated I SC excluding the involvement of Na+ absorption. Adenosine was found to have little effect on the I SC excluding the involvement of P1 receptors. The effect of UTP, a potent P2U receptor agonist on the I SC was similar to that of ATP while potent P2X agonist, α-β-Methylene adenosine 5′-triphosphate (α-β-M-ATP) and P2Y agonist, 2-methylthio-adenosine triphosphate (2-M-ATP), were found to be ineffective. The effect of ATP on I SC was mimicked by the Ca2+ ionophore, ionomycin, indicating a role of intracellular Ca2+ in mediating the ATP response. Confocal microscopic study also demonstrated a rise in intracellular Ca2+ upon stimulation by extracellular ATP. In voltage-clamped endometrial epithelial cells, ATP elicited a whole-cell Cl current which exhibited outward rectification and delayed activation and inactivation at depolarizing and hyperpolarizing voltages, respectively. The results of the present study demonstrate the presence of a regulatory mechanism involving extracellular ATP and P2U purinoceptors for endometrial Cl secretion.  相似文献   

11.
Agrobacterium rhizogenes A4M70GUS-mediated transformation of Savoy cabbage (Brassica oleracea L. var. sabauda) and two local lines of cabbage (B. oleracea L. var. capitata) was obtained using hypocotyl and cotyledon explants. The percentage of explants which formed roots was very high in all genotypes: 92.3 % in Savoy Gg-1, 64.4 % in cabbage P22I5, and 87.2 % in P34I5. Spontaneous shoot regeneration of excised root cultures grown on the hormone-free medium occurred in all three genotypes. In cabbage lines P22I5 and P34I5 shoot regeneration was higher (9.3 and 2.6 % respectively) than in Savoy cabbage Gg-1 (1.3 %). Transgenic nature of hairy root-derived plants was evaluated by GUS histological test and PCR analysis. All the tested cabbage shoots were GUS positive whilst in a Savoy cabbage GUS expression was registered only in 55 % of tested clones. PCR analysis demonstrated the presence of the GUS gene in regenerated shoot clones and in T1 progeny.  相似文献   

12.
Guo P  Su Y  Cheng Q  Pan Q  Li H 《Carbohydrate research》2011,(7):986-990
The 1:1 inclusion complex of β-cyclodextrin and p-aminobenzoic acid was prepared and characterized by TG-DTA. The crystal structure of the complex was solved directly from powder X-ray diffraction data using the direct space approach and refined using Rietveld refinement techniques. The complex crystallizes in monoclinic P21 space group, with unit cell parameters a = 20.7890 ?, b = 10.2084 ?, c = 15.1091 ?, β = 110.825°, V = 2997 ?3. The amino group is located at the wide side of the β-cyclodextrin cavity, forming hydrogen bonds with β-cyclodextrin, and the carboxyl group is located at the narrow side. The crystallographic data obtained from powder diffraction data were compared with the single crystallographic data, and the result shows that solving crystal structure of cyclodextrins inclusion complexes of such complexity is accessible to powder diffractionists to some extent.  相似文献   

13.
Sulphate uptake by the unicellular marine red algaRhodella maculata conforms to Michaelis-Menten kinetics. Two uptake systems have been found: a low affinity system with an apparentK m of 22 mM, and a high affinity system with an apparentK m of 63.4 M. Transition from the low to the high affinity system can occur within 2.5 min, in response to a decrease in the ambient sulphate concentration to below 10 mM. Assimilation rates in the dark are about 20% those in the light, although enhancement by light is independent of the quanlity of light supplied above 27 mol m-2 s-1. Use of metabolic inhibitors indicates that photophosphorylation provides the main source of energy for sulphate assimilation, through both cyclic and non-cyclic electron flow.Abbreviations used APS-kinase ATP:adenylyl-sulphate 3-phosphotransferase (E.C. 2.7.1.25) - ATP-sulphurylase ATP:sulphate adenylyltransferase (E.C.2.7.74) - DCMU [3-(3,4-dichlorophenyl)]-1,1 dimethylurea - 2,4 DNP 2,4-dinitrophenol - DBMIB Dibromothymoquinone (2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone)  相似文献   

14.
Fungal methionine synthase, Met6p, transfers a methyl group from 5-methyl-tetrahydrofolate to homocysteine to generate methionine. The enzyme is essential to fungal growth and is a potential anti-fungal drug design target. We have characterized the enzyme from the pathogen Candida albicans but were unable to crystallize it in native form. We converted Lys103, Lys104, and Glu107 all to Tyr (Met6pY), Thr (Met6pT) and Ala (Met6pA). All variants showed wild-type kinetic activity and formed useful crystals, each with unique crystal packing. In each case the mutated residues participated in beneficial crystal contacts. We have solved the three structures at 2.0–2.8 Å resolution and analyzed crystal packing, active-site residues, and similarity to other known methionine synthase structures. C. albicans Met6p has a two domain structure with each of the domains having a (βα)8-barrel fold. The barrels are arranged face-to-face and the active site is located in a cleft between the two domains. Met6p utilizes a zinc ion for catalysis that is bound in the C-terminal domain and ligated by four conserved residues: His657, Cys659, Glu679 and Cys739.  相似文献   

15.
The paper deals with a new form ofSinoadapis from the Lufeng hominoid Locality, assigned toSinoadapis shihuibaensis sp. nov. Holotype PA 882 A fragment of right mandible with C,−M3. Other materials. PA 903 A fragment of left maxilla with P3−M3. PA 959 Left lower tooth row with I1−P2, P4. PA 902 Right upper tooth row with C′−P3. PA 964 An isolated left I1. PA 907 An isolated right I3. PA 972 An isolated right M3.  相似文献   

16.
The structure of trypanosomal triosephosphate isomerase (TIM)has been solved at a resolution of 2.1Å in a new crystal form grown at pH 8.8 from PEG6000. In this new crystal form (space group C2, cell dimensions 94.8 Å, 48.3 Å, 131.0 Å, 90.0°, 100.3°, 90.0°), TIM is present in a ligand-free state. The asymmetric unit consists of two TIM subunits. Each of these subunits is part of a dimer which is sitting on a crystallographic twofold axis, such that the crystal packing is formed from two TIM dimers in two distinct environments. The two constituent monomers of a given dimer are, therefore, crystallographically equivalent. In the ligand-free state of TIM in this crystal form, the two types of dimer are very similar in structure, with the flexible loops in the “Open” conformation. For one dimer (termed molecule-1), the flexible loop (loop-6) is involved in crystal contacts. Crystals of this type have been used in soaking experiments with 0.4 M ammonium sulphate (studied at 2.4 Å resolution), and with 40 μM phosphoglycolohydroxamate (studied at 2.5 Å resolution). It is found that transfer to 0.4 M ammonuum sulphate (equal to 80 times the Ki of sulphate for TIM), gives rise to significant sulphate binding at the active site of one dimer (termed molecule-2), and less significant binding at the active site of the other. In neither dimer does sulphate induce a “closed” conformation. In a mother liquor containing 40 μM phosphoglycolohydroxamate (equal to 10 times the Ki of phosphoglycolohydroxamate for TIM), an inhibitor molecule binds at the active site of only that dimer of which the flexible loop is free from crystal contacts (molecule-2). In this dimer, it induces a closed conformation. These three structures are compared and discussed with respect to the mode of binding of ligand in the active site as well as with respect to the conformational changes resulting from ligand binding. © 1993 Wiley-Liss, Inc.  相似文献   

17.
A neutral lipase from the filamentous fungus Rhizopus delemar has been crystallized in both its proenzyme and mature forms. Although the latter crystallizes readily and produces a variety of crystal forms, only one was found to be suitable for X-ray studies. It is monoclinic (C2, a = 92.8 Å, b = 128.9 Å, c = 78.3 Å, β = 135.8) with two molecules in the asymmetric unit related by a noncrystallographic diad. The prolipase crystals are orthorhombic (P212121, with a = 79.8 Å, b = 115.2 Å, c = 73.0 Å) and also contain a pair of molecules in the asymmetric unit. Initial results of molecular replacement calculations using the refined coordinates of the related lipase from Rhizomucor miehei identified the correct orientations and positions of the protein molecules in the unit cells of crystals of both proenzyme and the mature form. © 1994 John Wiley & Sons, Inc.  相似文献   

18.
Bipyramidal crystals of the recombinant calmodulin from Trypanosoma brucei rhodesiense were obtained by vapor diffusion against 55% (v/v) 2-methyl-2,4-pentanediol in 0.05 M cacodylate buffer, pH 5.6. When few nucleation events occurred, crystals grew to 0.25 × 0.25 × 1.20 mm. The space group of the crystal is I4122, with unit cell dimensions a = b = 56.88 Å, c = 230.11 Å, α = β = γ = 90°, z = 16. The molecular mass and volume of the unit cell suggest that there is one molecule in the asymmetric unit. The I/σ(I) ratio for data at 3.0 Å resolution was 3.67, indicating that the final structure can be refined at higher resolution. Molecular replacement methods and the PC-refinement technique have not yet yielded the structure under a variety of search conditions. We are currently investigating the multiple isomorphous replacement approach to determine this crystal structure. © 1995 Wiley-Liss, Inc.  相似文献   

19.
The mammalian peptidoglycan recognition protein-S (PGRP-S) binds to peptidoglycans (PGNs), which are essential components of the cell wall of bacteria. The protein was isolated from the samples of milk obtained from camels with mastitis and purified to homogeneity and crystallized. The crystals belong to orthorhombic space group I222 with a = 87.0 Å, b = 101.7 Å and c = 162.3 Å having four crystallographically independent molecules in the asymmetric unit. The structure has been determined using X-ray crystallographic data and refined to 1.8 Å resolution. Overall, the structures of all the four crystallographically independent molecules are identical. The folding of PGRP-S consists of a central β-sheet with five β-strands, four parallel and one antiparallel, and three α-helices. This protein fold provides two functional sites. The first of these is the PGN-binding site, located on the groove that opens on the surface in the direction opposite to the location of the N terminus. The second site is implicated to be involved in the binding of non-PGN molecules, it also includes putative N-terminal segment residues (1-31) and helix α2 in the extended binding. The structure reveals a novel arrangement of PGRP-S molecules in which two pairs of molecules associate to form two independent dimers. The first dimer is formed by two molecules with N-terminal segments at the interface in which non-PGN binding sites are buried completely, whereas the PGN-binding sites of two participating molecules are fully exposed at the opposite ends of the dimer. In the second dimer, PGN-binding sites are buried at the interface while non-PGN binding sites are fully exposed at the opposite ends of the dimer. This form of dimeric arrangement is unique and seems to be aimed at enhancing the capability of the protein against specific invading bacteria. This mode of functional dimerization enhances efficiency and specificity, and is observed for the first time in the family of PGRP molecules.  相似文献   

20.
The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 in a new crystal form (space group P212121; unit cell parameters: a = 42.82 Å, b = 90.68 Å, and c = 139.82 Å) was determined by the X-ray molecular replacement method at the resolution of 2.7 Å. The protein folding and the stereochemistry of its antigen-binding site were comparatively analyzed.  相似文献   

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