A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime

Many small-molecule compounds have been shown to bind the peripheral anionic site (PAS) of acetylcholinesterase, but only a few have been shown by X-ray crystallography to induce specific structural changes in the enzyme. Here, an unexpected conformational change observed in the PAS upon the binding of an experimental bis-imidazolium oxime nerve-agent antidote is reported and the observed structures are correlated with measured binding and reactivation kinetics.

Accounting for partiality in serial crystallography using ray-tracing principles

Serial crystallography generates partial reflections from still diffraction images. Partialities are estimated with EVAL ray-tracing simulations, thereby improving merged reflection data to a similar quality as conventional rotation data.

Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein

Some interesting aspects of domain swapping, which is a unique method of protein oligomerization, are addressed, with the aim of understanding the role of interfaces and hinge regions in domain swapping.

Cap-domain closure enables diverse substrate recognition by the C2-type haloacid dehalogenase-like sugar phosphatase Plasmodium falciparum HAD1

Crystal structures of P. falciparum HAD1 in complex with three different substrates were solved in order to understand how cap-domain movement enables diverse substrate recognition by this sugar phosphatase.

Structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum

The crystal structure of the 34 kDa F-actin-bundling protein ABP34 from D. discoideum is reported.

An alternative RNA polymerase I structure reveals a dimer hinge

The crystal structure of RNA polymerase I in an alternative crystal form at 5.5 Å resolution with three dimers in a pseudo-heptagonal helical arrangement is reported. The angle between the monomers in the three dimers differs markedly from that in previously reported high-resolution structures.

Advances in molecular-replacement procedures: the REVAN pipeline

The REVAN pipeline for automatic protein crystal structure solution via molecular replacement and density-guided optimization algorithms is described.

Refining a model electron-density map via the Phantom Derivative method

The efficiency of the Phantom Derivative method, in its non-ab initio variant, has been checked using phases obtained via molecular-replacement methods as a starting point.

Structural insights into conformational switching in the copper metalloregulator CsoR from Streptomyces lividans

The structural changes associated with conformational switching in a copper-sensing metalloregulator are revealed. These highlight the importance of charge distribution in regulating DNA binding.

Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase

X-ray structural analysis of T. cruzi spermidine synthase was conducted to identify novel inhibitor-binding sites, including an allosteric site, and to elucidate inhibition mechanisms.

Crystallographic studies of two variants of Pseudomonas aeruginosa IMPDH with impaired allosteric regulation

High-resolution structures of a variant of an IMPDH enzyme with the regulatory CBS motifs deleted, as well as a point-mutation variant, have been solved and provide new insights into the allosteric behaviour and the octameric structure of the enzyme.

Structures of the methyltransferase component of Desulfitobacterium hafniense DCB-2 O-de­methylase shed light on methyltetra­hydro­folate formation

The first crystal structures of an O-demethylase methyltransferase protein in apo, THF-bound and MTHF-bound forms are reported. A conserved asparagine residue position is altered in favour of a putative proton-relay network.

Iron binding to human heavy-chain ferritin

Time-lapse crystal structures of human H-chain ferritin loaded with iron show the distribution of the substrate metal ion within the catalytic site. Comparison of these data with previously determined X-ray structures of R. catesbeiana M ferritin points to a number of shared and unshared features of the active sites of the two proteins that contribute to the ongoing debate on the possible existence of a universal mechanism for iron oxidation in all ferritins.

ARCIMBOLDO_LITE: single-workstation implementation and use

ARCIMBOLDO solves the phase problem through massive combination of small fragments and density modification. The use and performance of the single-workstation implementation is described.

Combining phase information in reciprocal space for molecular replacement with partial models

ARCIMBOLDO solves the phase problem starting from small model fragments placed in the asymmetric unit. Density modification aids in combining phase information from correct solutions to avoid a combinatorial explosion of sequential searches.

The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase

The catalytic mechanism and low pH optimum of C. bescii family 3 pectate lyase are explained.

Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8

The structure of the complex of NO66 and Rpl8 was solved in the native state and NO66 recognizes the consensus motif NHXH . Tetramerization is required for efficient substrate binding and catalysis by NO66.

Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin

Models of crystal structures deposited in the Protein Data Bank for protein complexes of cisplatin and carboplatin appear to have troubling crystallographic problems and exhibit significant departures from the known principles of chemistry. They may serve as examples of what should be improved in the deposition and presentation of macromolecular models and how to handle deposition of the results of re-refinement of crystallographic data.

Responses to Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin

A response to the article Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin [Shabalin et al (2015), Acta Cryst. D71, 1965–1979].

Response from Tanley et al. to Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin

A response to the article Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin [Shabalin et al (2015), Acta Cryst. D71, 1965–1979].

Response from Boal and Rosenzweig to Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin

A response to the article Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin [Shabalin et al (2015), Acta Cryst. D71, 1965–1979].