Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes

A method is presented for screening fragment libraries using acoustic droplet ejection to co-crystallize proteins and chemicals directly on micromeshes with as little as 2.5 nl of each component. This method was used to identify previously unreported fragments that bind to lysozyme, thermolysin, and trypsin.

A slow-forming isopeptide bond in the structure of the major pilin SpaD from Corynebacterium diphtheriae has implications for pilus assembly

Two crystal structures of the major pilin SpaD from C. diphtheriae have been determined at 1.87 and 2.5 Å resolution. The N-terminal domain is found to contain an isopeptide bond that forms slowly over time in the recombinant protein. Given its structural context, this provides insight into the relationship between internal isopeptide-bond formation and pilus assembly.

An improved integration method in serial femtosecond crystallography

An improved integration method enhances the quality of electron-density maps and decreases the number of diffraction patterns that are needed in serial femtosecond crystallography.

Structural basis of a novel activity of bacterial 6-pyruvoyltetra­hydropterin synthase homologues distinct from mammalian 6-pyruvoyltetra­hydro­pterin synthase activity

Crystal structures show how bacterial PTPS homologues possess an unusual activity that differs from that of mammalian PTPS enzymes.

IR laser-induced protein crystal transformation

A novel method and the associated instrumentation for improving crystalline order (higher resolution of X-ray diffraction and reduced mosaicity) of protein crystals by precisely controlled heating is demonstrated. Crystal transformation is optically controlled by a video system.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described.

Exploiting fast detectors to enter a new dimension in room-temperature crystallography

A departure from a linear or an exponential decay in the diffracting power of macromolecular crystals is observed and accounted for through consideration of a multi-state sequential model.

Sunitinib: from charge-density studies to interaction with proteins

The first comprehensive analysis of the sunitinib malate crystal structure and charge-density distribution in the context of sunitinib complexes with a series of protein kinases is reported. The aspherical atom databank approach, Hirshfeld surface analysis and quantum theory of atoms in molecules are used as a foundation for the investigations of interactions between an inhibitor and a protein.

Structural insight into glucose de­hydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium

The structure of a medium-chain dehydrogenase reductase-type glucose dehydrogenase showing narrow substrate specificity was determined, and the unique structural features of the enzyme were compared with those of a glucose dehydrogenase showing broad substrate specificity.

Structural analysis and insight into metal-ion activation of the iron-dependent regulator from Thermoplasma acidophilum

The crystal structure of T. acidophilum IdeR is reported.

Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy

High-resolution X-ray crystallography has been effectively combined with resonance Raman spectroscopy to `fingerprint' and validate different redox and ligand states in structures of Alcaligenes xylosoxidans cytochrome c′.

Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

The structures of Escherichia coli YmfB on its own and in complex with three sulfates and two manganese ions, when compared with the structures of other Nudix hydrolases such as MutT, Ap₄Aase and DR1025, provide insight into the unique hydrolysis mechanism of YmfB.

Structure of the ubiquitin-activating enzyme loaded with two ubiquitin molecules

The structure of a ternary complex consisting of the ubiquitin-activating enzyme Uba1 and two differently bound ubiquitin molecules has been determined by X-ray crystallography. For the first time, the formation of the ubiquitin-acyladenylate could be structurally visualized together with the attachment of a second ubiquitin covalently linked to the active-site cysteine of Uba1. Model-building studies provide insights into the recruitment of ubiquitin-conjugating enzymes.

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed.

Bacteriophage P22 tailspike: structure of the complete protein and function of the interdomain linker

A single mutation in the linker region renders intact P22 tailspike crystallizable, allowing analysis of the crystal structure of the complete tailspike at high resolution. The mutant protein is still functional, but has to be distorted to fit into a published cryo-EM map, and the structure suggests an important role of the highly conserved linker in intramolecular signal transmission.

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement

Flexible torsion angle-based NCS restraints have been implemented in phenix.refine, allowing improved model refinement at all resolutions. Rotamer correction and rotamer consistency checks between NCS-related amino-acid side chains further improve the final model quality.

Structural basis of sialidase in complex with geranylated flavonoids as potent natural inhibitors

The crystal structure of sialidase from C. perfringens, a pathogenic bacterium causing various gastrointestinal diseases, was determined in complex with a potent natural polyphenolic geranylated flavonoid-based inhibitor. The complex structure and comparative kinetic studies revealed that the geranyl group and C3′ hydroxyl group of the flavonoid backbone contribute to inhibition of the bacterial sialidase and generation of the stable enzyme–inhibitor complex.

A novel β-xylosidase structure from Geobacillus thermoglucosidasius: the first crystal structure of a glycoside hydrolase family GH52 enzyme reveals unpredicted similarity to other glycoside hydrolase folds

The first structure of a CAZy glycoside hydrolase family 52 enzyme, that of G. thermoglucosidasius β-xylosidase, reveals structural similarities to other families with which it shares less than 13% sequence identity. The substrate-bound complex confirms the active-site residues and is consistent with a retaining mechanism.

An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC

The crystal structure of KaiC from Thermosynechococcus elongatus allows insight into the different anatomies of the CI and CII ATPases.

Structure of a three-dimensional domain-swapped dimer of the Helicobacter pylori type IV secretion system pilus protein CagL

CagL mediates contact of the pathogen H. pylori with host-cell integrins. A domain-swapped structure of CagL shows the RGD motif to act as a hinge region embedded in a helix and reveals the structure of the functionally important C-terminus.

Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple reaction complexes

The seven crystal structures presented in this work represent the first multiple reaction complexes (GlcNAc/GalNAc, GlcNAc-1P/GalNAc-1P, ATP/ADP and Mg²⁺) of NahK in the lacto-N-biose (LNB)/galacto-N-biose (GNB) pathway, providing the molecular basis for the recognition of substrates and gaining insights into the catalytic mechanism at the molecular level.

The structure of a class 3 nonsymbiotic plant haemoglobin from Arabidopsis thaliana reveals a novel N-terminal helical extension

The first crystal structure of a class 3 nonsymbiotic plant haemoglobin is reported to 1.77 Å resolution. The structure revealed a novel N-terminal helical extension that participates extensively in the dimeric interface.

Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility

This work reports crystal structures of trimeric riboflavin synthase from the pathogen B. abortus both as the apo protein and in complex with several ligands of interest. It is shown that ligand binding drives the assembly of the unique active site of the trimer, and these findings are complemented by a detailed kinetic study on this enzyme, in which marked inhibition by substrate and product was observed.

In cellulo structure determination of a novel cypovirus polyhedrin

The crystal structure of a previously unsolved type of cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells.

Structure of the epimerization domain of tyrocidine synthetase A

The synthesis of nonribosomal peptides often introduces D-configured amino acids into the final products. The first crystal structure of the epimerization domain of a nonribosomal peptide synthetase reveals a bilobal architecture and implies a general acid–base mechanism for the L↔D isomerization of aminoacyl substrates.

The structure of a novel electron-transfer ferredoxin from Rhodopseudomonas palustris HaA2 which contains a histidine residue in its iron–sulfur cluster-binding motif

The crystal structure of the ferredoxin HaPuxC has been solved at 2.3 Å resolution.

Structure of human Bloom's syndrome helicase in complex with ADP and duplex DNA

The crystal structure of the human BLM helicase in complex with ADP and a 3′-overhang DNA duplex is reported.

Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved α-helix for Act1 binding and IL-17 signaling

Crystal structure of the SEFIR domain from human IL-17 receptor A provides new insights into IL-17 signaling.

Structural characterization of the apo form and NADH binary complex of human lactate de­hydrogenase

A crystal structure of the human lactate dehydrogenase A apo form suitable for ligand soaking and a NADH binary-complex structure are presented.

Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data

Here, new evidence is provided to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry averaging.

Structural and functional characterization of an Isd-type haem-degradation enzyme from Listeria monocytogenes. Corrigendum

A correction is made to the article by Duong et al. [(2014). Acta Cryst. D70, 615–626].