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May 2004 issue
Cover illustration: Core structure and electron-density isosurfaces for putative antimycobacterial compounds and substrate analogs targeting rmlC in the rhamnose biosynthetic pathway. The electrostatic potential, calculated by density functional theory, is colored white (highest, positive) to purple (lowest, negative) (p. 895). The image was rendered with CaChe WorkGroup Pro v6.1.1.
research papers
The light-harvesting chlorophyll a/b protein complex (LHC-II) from pea thylakoid membranes was co-crystallized with native lipids and the resultant octahedral crystal was investigated by X-ray crystallography and cryo-electron microscopy. The crystal was shown to be made up of proteoliposomes with a diameter of 254 Å, in each of which 20 trimers of LHC-II are arranged in a T = 1 icosahedral lattice.
The crystal structure of the C subunit of V-type H+-ATPase from T. thermophilus has been determined at 1.85 Å resolution. The overall structure is highly helix-rich with 20 α-helices, and 310-helices and the molecule is apparently composed of three similar domains.
PDB reference: C subunit of V0V1-ATPase, 1v9m
The structure of the C73G mutant of putidaredoxin (Pdx), the Fe2S2 ferredoxin that supplies electrons to cytochrome CYP101 (P450cam) for camphor oxidation, is reported at 1.9 Å resolution in a C2 crystal form.
PDB reference: C73G putidaredoxin, 1r7s, r1r7ssf
The structure of the complex formed between 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide and d(CGTACG)2 has been refined to a resolution of 1.55 Å. The complex structure is very similar to six published structures of intercalators bound to d(CGTACG)2 in the presence of cobalt. A detailed comparison of the structures is made.
PDB reference: 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide– d(CGTACG)2 complex, 1rqy, r1rqysf
NDB reference: DD0062
The crystal structures of two RNA octamers, 5′-GGC(GA)GCC-3′ and 5′-GIC(GA)GCC-3′, have been determined from X-ray diffraction data to 2.8 and 2.7 Å resolution, respectively.
The crystal structure of the extracellular xylanase from G. stearothermophilus T-6 has been determined and refined at 2.4 Å resolution, using selenomethionyl MAD initial phases. As for other family 10 xylanases, this enzyme is made of an eightfold TIM-barrel, with two catalytic carboxylic residues in geometry typical for `retaining' glycoside hydrolases.
PDB reference: xylanase, 1hiz, r1hizsf
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For 600 metal coordination groups of Ca, Mg, Mn, Fe, Cu, Zn, Na or K in a representative set of proteins from the Protein Data Bank, tables of composition and conformation are presented. For coordination groups of Ca and Zn the patterns found and the possibility of prediction are discussed.
Procedures for the effective application of singular value decomposition to experimental time-resolved macromolecular crystallographic data have yet to be explored systematically. In our application of singular value decomposition to a series of thirty time-resolved Laue data sets through the photocycle of the E46Q mutant of photoactive yellow protein, we develop protocols for analyzing the data in an unbiased manner and for addressing the substantial random and systematic errors present in it.
Crystals of the β-subunit of the luteinizing hormone were obtained from the intact hormone only in the presence of detergent and trypsin. The effects of proteolysis on crystallization are discussed.
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The crystal structure of feruloyl esterase from A. niger has been determined to a resolution of 1.5 Å. In addition, the structure of feruloyl esterase complexed with its product, ferulic acid, has been obtained at 1.08 Å resolution
In this paper, it is demonstrated that a new setup can be used on a synchrotron beamline to mount and centre the sample and to collect diffraction data. This new system completely changes the design of the experimental setup by merging functions that were previously considered to be distinct.
The 1.7 Å native structure of the dTDP-4-keto-6-deoxyglucose epimerase encoded by the M. tuberculosis rmlC gene is reported. RmlC, the third enzyme in the M. tuberculosis dTDP-L-rhamnose pathway, is essential for mycobacterial cell-wall synthesis and is a promising target for structure-guided drug design.
PDB reference: dTDP-4-keto-6-deoxyglucose epimerase, 1upi, r1upisf
structural genomics papers
The crystal structure of an osmotically inducible protein from E. coli confirmed the presence of a peroxiredoxin-like active site.
PDB reference: OsmC, 1nye, r1nyesf
crystallization papers
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The full-length β2 subunit of rat Kv1 K+ channel has been expressed in E. coli and crystallized. The crystals were shown to be perfectly pseudo-merohedrally twinned of the real space group P21212 with the apparent space group P4212.
The crystallization and structural studies of two bacterially expressed L. mexicana mexicana glucose-6-phosphate isomerase (PGI) molecular constructs are presented, representing the first kinetoplastid PGI to be crystallized. One form corresponds to the natural enzyme; the second form corresponds to a form from which the N-terminal extension has been removed.
The overproduction, purification and crystallization of the organic hydroperoxide-resistance protein from D. radiodurans are described. The crystals are monoclinic, space group P21, with unit-cell parameters a = 45.7, b = 59.6, c = 49.7 Å, β = 90.43°. Preliminary X-ray diffraction data have been collected.
NtcA from Anabaena PCC 7120 is a dimeric protein that consists of 223 amino acids with a molecular weight of 25 kDa per subunit. It belongs to the cAMP receptor-protein (CAP) family and is involved in the regulation of several of the genes acting in the nitrogen-fixation process. Here, the crystallization and preliminary X-ray data of NtcA are described.
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Crystals have been grown of the pneumococcal histidine triad protein PhtA and diffraction data collected to 1.2 Å.
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Crystals of BbCRASP-1, a borrelial protein that binds to human factor H and factor-H-like protein-1, have been grown and diffraction data to 2.7 Å collected. Data from SeMet-labelled crystals have also been collected (to 3.2 Å): these should allow phase determination and hence structure solution.
This paper reports the crystallization and preliminary X-ray analysis of two crystal forms of earthworm fibrinolytic enzyme component B, one of which was merohedrally twinned.
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Three contiguous EGF modules of EMR2, an EGF-TM7 molecule, have been overexpressed, purified and crystallized. An anomalous Patterson has been calculated using data from a Ba2+ co-crystal and phasing is now in progress.
A native chitinase from the fungal pathogen A. fumigatus YJ-407 (afCHI) has been crystallized. The crystals diffracted to 1.7 Å resolution and the structure was solved by the molecular-replacement method.
Ornithine cyclodeaminase is a bacterial protein that converts L-ornithine into L-proline plus ammonia and is a member of the μ-crystallin protein family. Here, the use of high-throughput crystallization methods leading to the preparation of X-ray diffraction-quality crystals of ornithine cyclodeaminase from Pseudomonas putida is described.
The crystallization and X-ray data collection to 2.4 Å of recombinant human vinculin head domain (residues 1–258) in complex with one of talin's vinculin-binding sites (residues 607–635) is reported.
Nicotinic acid mononucleotide adenylyltransferase from P. aeruginosa was crystallized and X-ray diffraction data were collected to 1.70 Å.
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A mutant of RR02, an essential response regulator from S. pneumoniae, has been crystallized and diffraction data have been collected to 1.93 Å.
The binary toxin produced by B. sphaericus was crystallized using PEG 4000 and NaCl. Native data extending to a resolution of 2.7 Å have been collected.
Methyl parathion hydrolase (MPH) from Pseudomonas sp. WBC-3, a zinc-containing enzyme that catalyzes the degradation of methyl parathion, has been purified and crystallized. A MAD data set has been collected to 2.5 Å resolution.
Xenobiotic reductase A catalyzes the regiospecific, NADPH dependent transformation of nitroglycerin to yield nitrite and 1,2-dinitroglycerol. This paper reports the crystallization and X-ray diffraction data analysis of the flavoenzyme.
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A soluble single-point mutant of Mos1 transposase has been expressed, purified and crystallized. Phase information has been obtained from a three-wavelength MAD data set collected at the selenium edge and a heavy-atom derivative.
A human VH fragment derived from the single-chain antibody scFvM12 has been crystallized and characterized at 1.8 Å resolution by X-ray diffraction.
A high-molecular-weight cytochrome containing 16 c-type haems has been purified from D. gigas cells and crystallized. The crystals diffracted to beyond 2.07 Å and a MAD data set was collected.
short communications
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A new crystal form of the `open' conformation of A. nidulans 3-dehydroquinate synthase has been grown following addition of substrate. The structure has been solved and refined to 1.7 Å resolution.
PDB reference: 3-dehydroquinate synthase, 1sg6, r1sg6sf
A novel L-amino-acid oxidase named AHP-LAAO with apoptosis-inducing activity was purified from A. halys pallas venom. Its crystal structure is similar to that of L-amino-acid oxidase from C. rhodostoma venom.
PDB reference: AHP-LAAO, 1reo, r1reosf
PilT pilus-retraction proteins from N. gonorrhoeae and A. aeolicus have been studied by electron microscopy and MAD-phased X-ray crystallography, respectively. A consistent picture emerges of a hexameric ring ultrastructure with a diameter of ∼110 Å and a height of ∼55 Å.
A simple software tool for cleaning up data from partially overlapping diffraction patterns is presented.
Some commercially available PEGs in the molecular-weight range 3000–8000 are contaminated with L-lactate. This result helps to explain the discovery of L-lactate bound in the active site of the E. coli PutA proline dehydrogenase domain crystal structure.
