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Molecular-replacement Methods (molecular-replacement + methods)
Selected AbstractsStructure of 3-deoxy- manno -octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy- manno -octulosonate in the ,-configurationACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2008Hye-Jin Yoon The enzyme 3-deoxy- manno -octulosonate cytidylyltransferase (CMP-KDO synthetase; CKS) catalyzes the activation of 3-deoxy- d - manno -octulosonate (or 2-keto-3-deoxy- manno -octonic acid; KDO) by forming CMP-KDO. CKS is unique to Gram-negative bacteria and is an attractive target for the development of antibacterial agents. The crystal structure of CKS from Haemophilus influenzae in complex with the substrate KDO has been determined at 2.30,Å resolution by combining single-wavelength anomalous diffraction and molecular-replacement methods. The two monomers in the asymmetric unit differ in the conformation of their C-terminal ,-helix (Ala230,Asn254). The KDO bound to the active site exists as the ,-pyranose form in the 5C2 chair conformation. The structure of CKS from H. influenzae in complex with KDO will be useful in structure-based inhibitor design. [source] Crystallization and preliminary X-ray analysis of candoxin, a novel reversible neurotoxin from the Malayan krait Bungarus candidusACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2003Palasingam Paaventhan Candoxin, a novel three-finger toxin from Bungarus candidus, is a reversible antagonist of muscle (,,,,) but a poorly reversible antagonist of neuronal ,7 nicotinic acetylcholine receptors. It has a molecular weight of 7344,Da, with 66 amino-acid residues including ten half-cystines. The fifth disulfide bridge is located at the tip of loop I (Cys6,Cys11) instead of in loop II as found in other ,-neurotoxins. Interestingly, candoxin lacks the segment cyclized by the fifth disulfide bridge at the tip of the middle loop of long-chain neurotoxins, which was reported to be critical for binding to ,7 receptors. As a first step to determining its three-dimensional structure, candoxin was crystallized by the hanging-drop vapour-diffusion technique in conditions around 1.5,M sodium chloride, 10%(v/v) ethanol. The crystals formed belonged to the hexagonal system, space group P6222, with unit-cell parameters a = 54.88, b = 54.88, c = 75.54,Å, , = , = 90, , = 120°, and diffract to a resolution of 1.80,Å. The crystallographic asymmetric unit contains one molecule of candoxin, with an estimated solvent content of 44.6%. Attempts to solve these structures by molecular-replacement methods have not been successful and a heavy-atom derivative search has been initiated. [source] Pushing the boundaries of molecular replacement with maximum likelihood.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2003Erratum In the calculations testing maximum-likelihood molecular-replacement methods reported in the paper by Read [(2001). Acta Cryst. D57, 13731382] simulated data constructed to test isomorphous replacement methods in the presence of known errors were used inadvertently. The test calculations have been repeated using the measured data, and the results are given. [source] Crystallization and preliminary X-ray analysis of bucain, a novel toxin from the Malayan krait Bungarus candidusACTA CRYSTALLOGRAPHICA SECTION D, Issue 10-2 2002L. Watanabe Bucain is a three-finger toxin, structurally homologous to snake-venom muscarinic toxins, from the venom of the Malayan krait Bungarus candidus. These proteins have molecular masses of approximately 6000,8000,Da and encompass the potent curaremimetic neurotoxins which confer lethality to Elapidae and Hydrophidae venoms. Bucain was crystallized in two crystal forms by the hanging-drop vapour-diffusion technique in 0.1,M sodium citrate pH 5.6, 15% PEG 4000 and 0.15,M ammonium acetate. Form I crystals belong to the monoclinic system space group C2, with unit-cell parameters a = 93.73, b = 49.02, c = 74.09,Å, , = 111.32°, and diffract to a nominal resolution of 1.61,Å. Form II crystals also belong to the space group C2, with unit-cell parameters a = 165.04, b = 49.44, c = 127.60,Å, , = 125.55°, and diffract to a nominal resolution of 2.78,Å. The self-rotation function indicates the presence of four and eight molecules in the crystallographic asymmetric unit of the form I and form II crystals, respectively. Attempts to solve these structures by molecular-replacement methods have not been successful and a heavy-atom derivative search has been initiated. [source] Structure of tetragonal crystals of human erythrocyte catalaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2001Martin K. Safo The structure of catalase from human erythrocytes (HEC) was determined in tetragonal crystals of space group I41 by molecular-replacement methods, using the orthorhombic crystal structure as a search model. It was then refined in a unit cell of dimensions a = b = 203.6 and c = 144.6,Å, yielding R and Rfree of 0.196 and 0.244, respectively, for all data at 2.4,Å resolution. A major difference of the HEC structure in the tetragonal crystal compared with the orthorhombic structure was the omission of a 20-residue N-terminal segment corresponding to the first exon of the human catalase gene. The overall structures were otherwise identical in both crystal forms. The NADPH-binding sites were empty in all four subunits and bound water molecules were observed at the active sites. The structure of the C-terminal segment, which corresponds to the last exon, remained undetermined. The tetragonal crystals showed a pseudo-4122 symmetry in molecular packing. Two similar types of lattice contact interfaces between the HEC tetramers were observed; they were related by the pseudo-dyad axes. [source] Challenging semi-bootstrapping molecular-replacement strategy reveals intriguing crystal packing of rhizavidinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2010Amit Meir The structure of rhizavidin, the first dimeric member of the avidin family which maintains high affinity towards biotin, was determined to high resolution by SeMet SAD. Consequently, the structure of the rhizavidin,biotin complex was determined by molecular-replacement methods using the apo structure as the search model; this ran into complications and required combined programs as well as bootstrapping approaches. Although present as a dimer in solution, rhizavidin packs as unique oligomers in both crystal forms. The novel insights derived from the unique molecular-replacement procedure and the crystal-driven oligomeric forms in this work may have utililty in biotechological and nanotechnological applications. [source] Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 9ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Matthew Mitchell Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8,Å resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0,Å. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetric unit capsid have been determined by molecular-replacement methods and structure determination is in progress. [source] | ||||||||||