The solvent component of macromolecular crystals

On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity.

Structure of ginseng major latex-like protein 151 and its proposed lysophosphatidic acid-binding mechanism

The crystal structure of ginseng major latex-like protein 151, its recognition of lysophosphatidic acid (LPA) and the activation of G protein-coupled LPA receptors by its complex with LPA are reported.

Ambiguity assessment of small-angle scattering curves from monodisperse systems

A method is presented to quantitatively assess the inherent ambiguity of three-dimensional shape reconstruction from a given small-angle scattering pattern.

REdiii: a pipeline for automated structure solution

The REdiii software pipeline allows fully automated crystal structure solution by embedding existing tools into a self-managing workflow.

Structures of Bacteroides fragilis uridine 5′-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (BfLpxA)

Ligand-free and UDP-N-acetylglucosamine-bound crystal structures of B. fragilis UDP-N-acetylglucosamine acyltransferase (BfLpxA) are reported.

Identification of local variations within secondary structures of proteins

ASSP is a freely available algorithm for secondary-structure assignment in protein structures. The algorithm is an extension of HELANAL-Plus and can be accessed at https://nucleix.mbu.iisc.ernet.in/assp/index.html.

Structural study of the X-ray-induced enzymatic reaction of octahaem cytochrome c nitrite reductase

X-ray-induced substrate (nitrite and sulfite) transformations are studied for cytochrome c nitrite reductase from T. nitratireducens.

Against the odds? De novo structure determination of a pilin with two cysteine residues by sulfur SAD

De novo structure determination by sulfur SAD (S-SAD) was achieved despite a low anomalous signal, radiation damage and low redundancy. Based on this case and statistics from S-SAD structures in the PDB threshold values for successful S-SAD structure determination are discussed.

Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity

MERS-CoV 3CL^pro has been crystallized and X-ray crystal structures have been solved in three different crystal forms representing the free enzyme structure and the enzyme–product complex.

Development of a Thermofluor assay for stability determination of membrane proteins using the Na⁺/H⁺ antiporter NhaA and cytochrome c oxidase

The use of the Thermofluor assay for membrane proteins was explored by testing five different detergents with common fluorescent probes. The dye 1-anilinonaphthalene-8-sulfonic acid was identified as a valuable tool when working with detergents and the membrane protein NhaA.

Three-dimensional structure and ligand-binding site of carp fishelectin (FEL)

The fishelectins (FELs) are a protein family first identified in carp eggs and now recognized to be present in fish and amphibians. Here, the X-ray structure of carp FEL is reported both in its apo form and bound to the α- and β-anomers of N-acetylglucosamine. This is the first experimentally determined structure of a member of this protein family.

Structural insight into the thermostable NADP⁺-dependent meso-di­aminopimelate de­hydrogenase from Ureibacillus thermosphaericus

The unique structure of thermostable meso-diaminopimelate dehydrogenase from U. thermosphaericus was determined and compared with those of corresponding enzymes from other sources.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics.

Structural and functional analysis of betaine aldehyde de­hydrogenase from Staphylococcus aureus

The purified putative betaine aldehyde dehydrogenase SACOL2628 from the early methicillin-resistant S. aureus COL has betaine aldehyde dehydrogenase activity and is structurally similar to aldehyde dehydrogenases.

Structural insights into the binding of the human receptor for advanced glycation end products (RAGE) by S100B, as revealed by an S100B–RAGE-derived peptide complex

The 2.55 Å resolution crystal structure of S100B in complex with a 15-amino-acid peptide derived from the receptor for advanced glycation end products is reported.

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced.

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1.

The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A–PKC412 complex reveals di­sulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine

The crystal structure of DYRK1A in complex with PKC412 and data for the binding of PKC412 to DYRK1A/1B are reported. This structure confirms the unique ability of DYRK kinases to form a disulfide bridge between the catalytic loop and the activation segment.

Structural basis for the catalytic mechanism of homoserine de­hydrogenase

The structure of S. aureus homoserine dehydrogenase at different pH conditions provides a basis for understanding the role of a lysine residue (Lys105) in the hydride-transfer step of the reaction mechanism.