FLEXR: automated multi-conformer model building using electron-density map sampling

Alternative conformations are underrepresented in current PDB models due to difficulties in manually detecting, building and inspecting multiple conformers. To overcome this shortcoming, an automated multi-conformer modeling program, FLEXR, has been developed that uses Ringer-based electron-density sampling to explicitly build multi-conformer models for refinement.

GEMMI and Servalcat restrain REFMAC5

The restraint-generation part of the macromolecular atomic model-refinement program REFMAC5 has been delegated to GEMMI. A controller program was implemented in Servalcat to distribute tasks between GEMMI and REFMAC5.

The T₂ structure of polycrystalline cubic human insulin

Characterization of the polymorphism of human insulin upon pH variation and structure determination of the cubic polymorph via Rietveld refinement are reported.

Structural and functional characterization of a multi-domain GH92 α-1,2-mannosidase from Neobacillus novalis

The structure of the full-length multi-domain GH92 α-1,2-mannosidase from N. novalis (NnGH92) was solved and the function of the noncatalytic domains was investigated by their sequential deletion and biochemical characterization of the NnGH92 variants. This work significantly advances the structural knowledge of multi-domain GH92 α-1,2-mannosidases and provides a better understanding for the future optimization of these enzymes for the degradation of yeast α-mannan or protein glycans.

Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases

The bond-valence method with weighting schemes statistically concludes that the reduction of P-clusters to P^N clusters by two electrons corresponds to a double protonation with decoordination of the serine residue and the peptide chain of cysteine in MoFe proteins.

Conformational transition of the Ixodes ricinus salivary serpin Iripin-4

The crystal structures of two important conformations of a new serpin from I. ricinus, namely the partially stressed native and cleaved conformations, were solved at 2.3 and 2.0 Å resolution, respectively. The importance of the reactive-centre loop in protease inhibition was also confirmed.

SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology

Scattering Contrast Match Points with Explicit-atom Deuteration (SCOMAP-XD) is a computational workflow that uses atomistic simulations with explicit deuteration to calculate contrast-match points and scattering vector-dependent contrast effects for the optimal design of small-angle neutron scattering experiments.

Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone

The structure of a complex between BRIL and an anti-BRIL antibody (SRP2070Fab) has been determined at high resolution. This work presents a detailed elucidation of the interaction between BRIL and SRP2070Fab, which may help to improve the function of SRP2070Fab as a crystallization chaperone for membrane proteins.

Alexei Vagin (1944–2023)

Alexei Vagin is remembered.