Changing of the guard

Physical aspects of protein crystal growth investigated with the Advanced Protein Crystallization Facility in reduced-gravity environments

Physicochemical insights into protein crystallization investigated with the Advanced Protein Crystallization Facility are critically reviewed.

Structure of the N-terminal domain of human FKBP52

The structure of the N-terminal domain of human FKBP52 was determined using molecular replacement to 2.4 Å. The overall structure is very similar to FKBP12, and the structure–functional relationship of the protein is discussed.

Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis

The structure of an enzyme involved in the non-mevalonate pathway of isoprenoid synthesis in the thermophilic bacterium Thermus thermophilus has been solved to high resolution in the presence of substrate and with a substrate analogue.

Is the bond-valence method able to identify metal atoms in protein structures?

The calcium bond-valence sum (CBVS) is proposed as a convenient way of identifying metal ions in protein structures.

Automated main-chain model building by template matching and iterative fragment extension

A method for automated macromolecular main-chain model building is described.

Automated side-chain model building and sequence assignment by template matching

A method for automated macromolecular side-chain model building and for aligning the sequence to the map is described.

Three-dimensional structure of homodimeric cholesterol esterase–ligand complex at 1.4 Å resolution

The 1.4 Å resolution three-dimensional structure of a homodimeric cholesterol esterase (Candida cylindracea) in complex with an unknown ligand revealed the presence of a C₂₃-chain fatty acid in an elongated enzyme active site.

Locating the anomalous scatterer substructures in halide and sulfur phasing

The phasing of proteins using the anomalous signal from inherent sulfur or halides in the solvent requires the coordinates of an appreciable number of partially occupied or weak sites to be determined. The use of dual-space recycling methods, as implemented in the program SHELXD, to solve such anomalous scatterer substructures in MAD, SAD, SIR and SIRAS experiments has been tested on a previously unknown protein structure.

Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA

An A-DNA decamer at 1.25 Å resolution shows a novel binding mode of cobalt hexammine ion to DNA duplexes. Analysis of thermal parameters (B factors) indicates that nucleotides involved in abutting crystal packing are thermally more stable than other nucleotdes in the duplex.

Structure of Escherichia coli uridine phosphorylase at 2.0 Å

The 2.0 Å resolution crystal structure of E. coli uridine phosphorylase suggests greater structural similarity to E. coli purine phosphorylase, lending further support to the hypothesis that members of the related but functionally distinct NP-I enzyme class evolved from a common ancestor.

A rapid method for assessing lipid:protein and detergent:protein ratios in membrane-protein crystallization

A simple rapid method using infrared spectroscopy for measuring lipid:protein ratios and detergent concentrations in solubilized integral membrane-protein samples has been developed. This analytical tool will aid in the purification and solubilization of membrane proteins that are ideal for crystallization trials.

Atomic resolution structure of Erwinia chrysanthemi L-asparaginase

The crystal structure of E. chrysanthemi L-asparaginase has been refined at 1.0 Å resolution, elucidating the atomic level details of one of the largest asymmetric units studied to date at this level of accuracy.

The refined atomic structure of carbonic anhydrase II at 1.05 Å resolution: implications of chemical rescue of proton transfer

Using synchrotron radiation and a CCD detector, X-ray data have been collected at 100 K for the His64Ala mutant of human carbonic anhydrase II complexed with 4-methylimidazole (4-MI) to a maximal 1.05 Å resolution, allowing full anisotropic least-squares refinement.

Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 Å) at 100 K and atomic resolution (1.11 Å) at 293 K refined anisotropically to small-molecule accuracy

The structure of T. aurantiacus xylanase solved to small-molecule accuracy at atomic resolution (1.11 Å) at 293 K and at ultrahigh resolution (0.89 Å) at 100 K provides insights into the plasticity of salt bridges, the temperature-dependent deformation and the water structure of the enzyme, which belongs to the ubiquitous TIM-barrel fold.

A new class of gadolinium complexes employed to obtain high-phasing-power heavy-atom derivatives: results from SAD experiments with hen egg-white lysozyme and urate oxidase from Aspergillus flavus

Seven gadolinium complexes are shown to be excellent compounds for the production of heavy-atom derivatives for macromolecular crystallography projects. SAD phasing has been successfully carried out on a series of gadolinium-derivative crystals of two proteins, hen egg-white lysozyme and urate oxidase from A. flavus, leading to high-quality electron-density maps.

Structure of a yeast hypothetical protein selected by a structural genomics approach

The crystal structure of YBL036C has been determined by MIRAS and MAD methods.

Crystals of trp repressor suitable for high-resolution neutron Laue diffraction studies

Preliminary neutron-diffraction measurements of E. coli trp repressor crystals demonstrate that it will be possible to obtain a full-atom neutron structural model of a DNA-binding protein plus its associated solvent.

Crystallization and preliminary X-ray analysis of Ali­cyclobacillus acidocaldarius endoglucanase CelA

Crystallization of family 9 A. acidocaldarius CelA is reported. The crystals are unusual in that they do not bind the dye IZIT in the mother liquor and do not dissolve in the protein-storage buffer or water for several weeks. Collection of a data set to 3.0 Å resolution and initial molecular-replacement searches are reported.

Crystallization and X-ray diffraction analysis of an all-RNA U₃₉C mutant of the minimal hairpin ribozyme

An all-RNA 64-mer hairpin ribozyme has been crystallized in a form suitable for X-ray diffraction analysis at 3.35 Å resolution. The construct contains the U₃₉C substitution, which enhances catalytic efficiency and represents the minimal catalytic motif formed by intermolecular docking of two helix–loop–helix domains. The crystallization strategy and results are presented.

Crystallization and preliminary crystallographic analysis of a partial extracellular fragment of a sperm membrane protein YWK-II/APPH related to the Alzheimer βA4-amyloid precursor protein

A partial extracellular fragment of a sperm membrane protein YWK-II protein/APPH related to the Alzheimer βA4-amyloid precursor protein has been recloned, expressed in E. coli, crystallized and a complete native data set has been collected at 2.8 Å resolution.

Expression, crystallization and preliminary X-ray analysis of isomaltulose synthase (PalI) from Klebsiella sp. LX3

The first crystallographic study, at 2.2 Å resolution, of an enzyme that is involved with both hydrolysis and isomerization of sucrose.

Preliminary X-ray crystallographic analysis of tRNA pseudouridine 55 synthase from the thermophilic eubacterium Thermotoga maritima

Overexpression, purification and crystallization of T. maritima TruB allowed collection of a complete data set to 2.0 Å resolution.

Crystallization of the GTP-dependent transcriptional regulator CodY from Bacillus subtilis

The GTP-responsive transcriptional repressor CodY from B. subtilis has been crystallized in a number of forms in the presence and absence of ligands. A complete data set to 3.5 Å spacing has been collected.

X-ray analysis of two antibiotic-synthesizing bacterial ester hydrolases: preliminary results

Good-quality crystals have been obtained of two microbial α-amino-acid ester hydrolases, enzymes of potential use in antibiotic production. One enzyme crystallizes in two space groups, one of which has extremely large unit-cell parameters.

Jel44 monoclonal Fab fragment specific for HPr of the phosphoenolpyruvate:sugar phosphotransferase system of Escherichia coli and the complex of Jel44 Fab fragment with HPr: preparation, crystallization and preliminary crystallographic analysis

A Jel44 monoclonal Fab fragment specific for E. coli HPr has been purified. Crystals of the Jel44 Fab fragment diffracted to a resolution of 4.6 Å, while crystals of the novel complex of the Jel44 Fab fragment with HPr diffracted to a resolution of 2.5 Å.

Crystallization and preliminary X-ray studies of thymus and activation-regulated chemokine (TARC)

Preliminary crystallographic studies of synthetically prepared thymus and activation-regulated chemokine (TARC) in the triclinic, hexagonal and tetragonal systems are described.

Crystallization and preliminary X-ray crystallographic analysis of malonyl-CoA de­carboxylase from Rhizobium leguminosarum bv. trifolii

Malonyl-CoA decarboxylase of a Rhizobium species was crystallized. This enzyme shares 30% sequence identity with human homology.

SseA, a 3-mercaptopyruvate sulfurtransferase from Escherichia coli: crystallization and preliminary crystallographic data

The in vivo role and substrate specificity of sulfurtransferase enzymes has been greatly debated. SseA, a 3-mercaptopyruvate:cyanide sulfurtransferase from E. coli, has been crystallized in a tetragonal crystal form suitable for X-ray crystallographic investigations.

Crystallization and preliminary X-ray diffraction studies of Hje, a Holliday junction resolving enzyme from Sulfolobus solfataricus

The Holliday junction resolving enzyme Hje from S. solfataricus has been crystallized. Preliminary crystallographic analysis indicates a possible difference in dimeric arrangement to the homologous enzyme Hjc.

Crystallization and preliminary X-ray diffraction studies of a novel alcohol de­hydrogenase from the hyperthermophilic archaeon Aeropyrum pernix

Crystals of a zinc-containing alcohol dehydrogenase from the hyperthermophilic archaeon A. pernix have been grown by the sitting-drop vapour-diffusion technique from recombinant protein expressed in E. coli and show diffraction to 1.5 Å resolution. The anomalous diffraction from zinc at two wavelengths and twofold NCS averaging have resulted in an interpretable electron-density map.

Crystallographic characterization of the radixin FERM domain bound to the C-terminal region of the human Na⁺/H⁺-exchanger regulatory factor (NHERF)

Crystals of complexes between the radixin FERM domain and the C-terminal regions of NHERF and NHERF2 have been obtained.

Crystallization and preliminary X-ray crystallographic studies of 3-de­oxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae

CMP-KDO synthetase from H. influenzae was crystallized. X-ray diffraction data were collected to 2.2 Å from an SeMet crystal.

Crystallization and preliminary X-ray crystallographic analysis of tRNA(m¹G37)methyltransferase from Haemophilus influenzae

tRNA(m¹G37)methyltransferase (TrmD) from H. influenzae was crystallized. X-ray data have been collected to 1.85 Å.

Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex

A phage T7 RNA polymerase elongation complex containing 8 bp of RNA–DNA hybrid and 10 bp of downstream DNA with a total molecular mass of ∼110 kDa was crystallized. A complete diffraction data set was collected at 2.6 Å resolution. The structure determination and refinement are in progress.

Preliminary crystallographic analysis of 3-chlorocatechol 1,2-dioxygenase of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol

3-Chlorocatechol 1,2-dioxygenase from the Gram-positive bacterium R. opacus (erythropolis) 1CP, an enzyme involved in the specific cleavage of 3-chlorocatechol, which is an intermediate in the aerobic biodegradation of 2-chlorophenol, has been crystallized.

Crystallization and preliminary crystallographic analysis of the kinase-recruitment domain of the PP2C-type phosphatase RsbU

The kinase-recruitment domain of the PP2C-type phosphatase RsbU from B. subtilis has been crystallized in a form that diffracts to 1.6 Å resolution using synchrotron radiation.

Application of a two-liquid system to sitting-drop vapour-diffusion protein crystallization

A new method of protein crystallization, the floating-drop vapour-diffusion technique, has been developed.

Notes for authors 2003