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January 2002 issue
Cover illustration: The molecular surface of the homohexameric allosteric enzyme glucosamine-6-phosphate deaminase from E. coli, showing aproaching views of the active and allosteric sites during the alosteric transition process, where the role of the structural flexibility is crucial. The protein surface is colored according to the behaviour during the allosteric transition: cyan, the internal zone; yellow the external zone and magenta, the active-site lid (p. 10).
research papers
A neutral gadolinium complex, Gd-HPDO3A, is shown to be a good candidate to obtain heavy-atom derivatives and solve macromolecular structures using anomalous dispersion. Tetragonal crystals of a gadolinium derivative of hen egg-white lysozyme were obtained by co-crystallization using different concentrations of the complex. Diffraction data from three derivative crystals were collected to a resolution of 1.7 Å using Cu Kα radiation from a rotating anode.
PDB reference: Gd derivative of lysozyme, 1h87
A new crystallographic structure of the free active-site R conformer of the allosteric enzyme glucosamine-6-phosphate deaminase from Escherichia coli, coupled with previously reported structures of the T and R conformers, generates a detailed description of the heterotropic allosteric transition in which structural flexibility plays a central role.
PDB references: R form glucosamine-6-phosphate deaminase complex with fructose 6-phosphate at 2.15 Å, 1fqo; R form glucosamine-6-phosphate deaminase complex with N-acetyl-glucosamine-6-phosphate at 2.10 Å, 1frz; R form glucosamine-6-phosphate deaminase complex with N-acetyl-glucosamine-6 phosphate at 1.73 Å, 1fs5; T form glucosamine-6-phosphate deaminase at 2.2 Å, 1fs6; T form glucosamine-6-phosphate deaminase at 1.9 Å, 1fsf
The structures of two crystal forms of tryparedoxin II from C. fasciculata have been determined de novo by exploiting the anomalous scattering at 1.77 Å wavelength of the S atoms in the native protein.
The first structure of a bacterioferritin from a photosynthetic organism (R. capsulatus) was solved by the MIR method at 2.6 Å resolution in the I422 space group and compared with that from E. coli solved in the P21 and P42212 space groups. The new crystals reveal for the first time the presence of the non-symmetric heme molecule on a twofold crystallographic axis. It is concluded that in the crystal each heme site contains a symmetrical mixture of heme in two orientations.
PDB reference: bacterioferritin, 1jgc
P3 is a trimer of double viral jelly rolls and so has an architecture similar to hexon, its counterpart in the mammalian adenovirus. The X-ray structure at 1.65 Å resolution shows flexible loops at locations important for capsid interactions and an intricate water network that appears to contribute additional stability to the `trimerization loops' at the top of the molecule.
The use of xenon and krypton as hydrophobic probes to distinguish between aqueous and detergent solvent regions in crystals of the membrane protein OmpF porin by conventional X-ray crystallography is assessed.
The X-ray structures of rabbit and porcine serum transferrins are reported at resolutions of 2.6 and 2.15 Å, respectively. The more acid-labile release of iron from serum transferrins than from lactoferrins is discussed.
Crystal structures of the nitric oxide reductase cytochrome P450nor in the ferric resting and the ferrous carbonmonoxy (CO) states have been determined at 1.00 and 1.05 Å resolution, respectively.
The sine-enhanced minimal function and the corresponding sine-enhanced Shake-and-Bake procedure have been proposed and tested. With proper choice of parameter values, the sine-enhanced Shate-and-Bake procedure outperformed the traditional Shake-and-Bake by a two- to eightfold increase in success rate for Se-atom substructures.
A novel approach for de novo phase determination using site-directed mutagenesis to generate noble-gas binding sites in proteins is described. MIR phases from xenon derivatives obtained using this method compare favorably with MAD phases from selenomethionine substitution.
The structure of an acidic PLA2 from D. acutus been determined by molecular replacement with significant conformational differences observed in segment 14–23 of the two molecules in the asymmetric unit. This segment is related to the interface recognition site.
PDB reference: acidic phospholipase A2, 1ijl
The structure of the glycoprotein rhamnogalacturonan acetylesterase has been refined at 1.12 Å resolution. The branched N-linked glycan structure has been refined without target values for bond lengths and angles and the resulting values are compared with the current dictionary values obtained from small-molecule studies.
PDB reference: rhamnogalacturonan acetylesterase, 1k7c
crystallization papers
The Zα domain of human ADAR1 has been cocrystallized with the chimeric oligonucleotide (dCrG)3 in the Z-conformation.
Ribosome recycling factor from E. coli has been crystallized in space group P21 with no additives. Data were collected to 2.2 Å and molecular replacement gave solutions for the rotation and translation functions.
SeMet S100A4 (human) has been crystallized using similar conditions to those used for the native protein. SeMet S100A4 crystals diffract better than the native for data collection and belong to space group P6 or P3.
E. coli L-asparaginase II with a Asp90Glu mutation in the active site has been crystallized in five polymorphic forms.
Phosphoserine phosphatase, a human enzyme involved in the L-serine biosynthesis pathway, has been purified and crystals suitable for structural analysis have been obtained.
The human and rabbit 20α-hydroxysteroid dehydrogenases, which catalyse the inactivation of progesterone, have been expressed in E. coli, purified and subsequently crystallized. Several crystal complexes have been obtained and three of them diffract to better than 2.0 Å resolution.
The human form of nicotinamide mononucleotide adenylyltransferase which catalyses the final step in the synthesis of nicotinamide-adenine dinucleotide (NAD+) by transferring the adenylyl moiety of ATP to nicotinamide mononucleotide with the release of pyrophosphate has been crystallized in the presence of NAD+.
An invertebrate C-type lectin, CEL-I, from the marine invertebrate C. echinata was crystallized and 2.0 Å resolution data were collected using synchrotron radiation.
Two dimeric disintegrins named PVS and acostatin were crystallized and data were collected to 2.0 and 2.8 Å resolution, respectively.
Scytalone dehydratase Phe162Ala variant is a good target for investigating the substrate-binding mechanism of the enzyme. the variant enzyme was crystallized in its unligated state, and the diffraction data of the crystal were collected at 37 K using synchrotron X-rays.
Crystallization of a large single crystal of a B-DNA decamer, d(CCATTAATGG), for a neutron-diffraction experiment has been accomplished by an analysis of its solubility phase diagram and a large single crystal was successfully crystallized at around the minimum solubility point of the oligonucleotide.
Dihydroorotase from the extreme hyperthermophile A. aeolicus was cloned and expressed at high levels in E. coli. Crystals of the purified wild type and selelnomethionine-substituted enzyme, space group C2, diffracted to a resolution of 1.7 Å.
Catalase–peroxidase from Synechococcus PCC 7942 has been purified and crystallized in the tetragonal space group P41212 or P43221. A native data set has been collected to 2.3 Å resolution using the SPring-8 synchrotron-radiation source.
A membrane-protein complex, formate dehydrogenase-N from E. coli, has been purified and crystallized.
Hexagonal crystals of dimeric dihydrodiol dehydrogenase from monkey were grown from buffered ammonium phosphate solutions. This is the first crystallization report of a dimeric dihydrodiol dehydrogenase.
The crystallization of soluble FAD-dependent α-glycerophosphate oxidase from Streptococcus sp. is reported. Synchrotron X-ray radiation was used to collect diffraction data to 2.4 Å resolution.
Crystallization and preliminary X-ray diffraction analysis of P. platycephala lectin, a Mimosoideae regarded as the most primitive group of Leguminosae plants, are reported. Resolution of this structure will show the arrangement of three tandem beta-prism domains, a novel architecture for a leguminous lectin.
The protease domain of T. maritima HtrA has been purified and crystallized. The crystals diffracted to 2.7 Å resolution.
C1027 is a macromolecular antitumour antibiotic produced by Streptomyces globispourus C1027 and consists of an apoprotein and a non-protein labile chromophore. The purified C1027 was monodisperse according to dynamic light-scattering measurements and crystallized in two different crystal forms from two different starting conditions using the vapour-diffusion method.
Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. The enantioselective halohydrin dehalogenase HheC from A. radiobacter AD1 was crystallized and data were collected to 3.0 Å resolution.
Acyl carrier protein synthase (acpS) catalyzes the formation of holo-ACP, which mediates the transfer of acyl fatty-acid intermediates during the biosynthesis of fatty acids and lipids. The M. tuberculosis enzyme has been expressed and purified, and then crystallized by the vapour-diffusion method using 2-propanol as a precipitant.
A thermostable lipase from B. stearothermophilus P1 has been overexpressed, purified and crystallized.
Porcine insulin has been crystallized as a monomer in the presence of 20% acetic acid. X-ray data has been collected to 1.6 Å resolution.
addenda and errata
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