Identifying, studying and making good use of macromolecular crystals

As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed.

Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP

In this study, the crystal structure of Saccharomyces cerevisiae mitochondrial Qri7 complexed with AMP (a part of threonylcarbamoyl-adenylate) has been determined at 2.94 Å resolution in a new crystal form.

Structures of a human blood group glycosyltransferase in complex with a photo-activatable UDP-Gal derivative reveal two different binding conformations

The structure of AA(Gly)B, a dual-specificity blood group synthase, in complex with UDP-galactose, the O6′′ atom of which is protected by an 2-nitrobenzyl group, has been determined in two space groups. The so-called caged substrate exhibits various distinct conformations in the active site.

The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain

The structure of the catalytic domain of RpfC (Rv1884) closely resembles those of RpfB and RpfE. This structural conservation highlights the importance of the versatile domain composition of the RPF family.

Crystal and solution structure of the human RIG-I SF2 domain

The crystal structure of the human RIG-I helicase domain, a key player protein in the antiviral innate immune response, is reported.

The structure of α-haemoglobin in complex with a haemoglobin-binding domain from Staphylococcus aureus reveals the elusive α-haemoglobin dimerization interface

The α chain of haemoglobin (α) has been crystallized as a homodimer bound to a domain from the S. aureus haemoglobin receptor iron-regulated surface determinant H (IsdH). This is the first X-ray crystal structure that captures the weak self-association interface of α.

Cloning, purification and preliminary crystallographic analysis of Ara127N, a GH127 β-L-arabino­furanosidase from Geobacillus stearothermophilus T6

A GH127 β-L-arabinofuranosidase from G. stearothermophilus T6 (Ara127N) has been purified and crystallized in two different crystal forms. A full X-ray diffraction data set was measured for the wild-type enzyme in a P2₁2₁2₁ crystal form (2.3 Å resolution) and complete MAD data were measured for the selenomethionine derivative in a P2₁ crystal form (2.5 Å resolution) to be used for the detailed three-dimensional structural analysis of the Ara127N protein.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of D-lactate de­hydrogenase from Lactobacillus jensenii

D-Lactate dehydrogenase from L. jensenii (LjD-LDH), a key enzyme for the production of the D-form of lactic acid from pyruvate, has been crystallized and X-ray diffraction data were collected from the crystal and analyzed.

Expression, purification and crystallization of pecan (Carya illinoinensis) vicilin

The crystallization of a putative food allergen from pecan is reported.

Preliminary X-ray crystallographic studies of the TIR domain of human Toll-like receptor 6

The human TLR6 TIR domain was crystallized and crystals were found to belong to space group C2, with unit-cell parameters a = 127.60, b = 44.20, c = 75.72 Å, β = 118.89°. The crystals were obtained at 20°C and diffracted to a resolution of 2.2 Å.

Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans

YidC, a membrane-protein chaperone/insertase from B. halodurans, was expressed, purified and crystallized in the lipidic cubic phase. An X-ray diffraction data set was collected to 2.4 Å resolution.

Overexpression, crystallization and preliminary X-ray characterization of Ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an uncharacterized CBM-containing protein

The R. flavefaciens scaffoldin C cohesin complexed with the dockerin from a CBM-containing protein has been crystallized. Data were collected to 2.5, 2.4 and 2.16 Å resolution from three different crystalline forms.

Overexpression, purification, crystallization and preliminary X-ray characterization of the fourth scaffoldin A cohesin from Acetivibrio cellulolyticus in complex with a dockerin from a family 5 glycoside hydrolase

The fourth scaffoldin A cohesin complexed with the dockerin of a family 5 glycoside hydrolase from A. cellulolyticus has been purified and crystallized, and data were processed to a resolution of 1.57 Å in space group P2₁2₁2₁.

Crystallization and preliminary crystallographic study of human coronavirus NL63 main protease in complex with an inhibitor

This article describes preliminary crystallographic data of a complex consisting of human coronavirus NL63 main protease and its inhibitor N3.

Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus, Amphi-IgSF-V

X-ray diffraction data for Amphi-IgSF-V (a single variable domain of the immunoglobulin superfamily from amphioxus) were collected to 1.95 Å resolution. The crystal belonged to space group P3₂21, with unit-cell parameters a = b = 53.9, c = 135.5 Å, and contained two molecules in the asymmetric unit. The Matthews coefficient and solvent content were calculated to be 2.58 ų Da⁻¹ and 52.38%, respectively.

Expression, high-pressure refolding, purification, crystallization and preliminary X-ray analysis of a novel single-strand-specific 3′–5′ exonuclease PhoExo I from Pyrococcus horikoshii OT3

A single-strand-specific 3′–5′ exonuclease, PhoExo I, from the hyperthermophilic archaeon P. horikoshii OT3 was produced as inclusion bodies in E. coli cells, solubilized by the high-pressure refolding method, purified and crystallized. The crystal of PhoExo I diffracted X-rays to 1.52 Å resolution.

Crystallization and X-ray diffraction of virus-like particles from a piscine betanodavirus

This is the first report of the crystallization conditions for VLPs from a grouper fish nervous necrosis virus, and the VLP structure diffracted X-rays to 7.5 Å with high completeness.

Crystallization and preliminary X-ray crystallographic analysis of the complex between the N-D1 domain of VCP from Homo sapiens and the N domain of OTU1 from Saccharomyces cerevisiae

The N-D1 domain of human VCP was crystallized in complex with the N domain of yeast OTU1 and X-ray diffraction data were collected to 3.25 Å resolution.

Purification, crystallization and preliminary X-ray crystallographic studies of Rv3705c from Mycobacterium tuberculosis

The cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of Rv3705c from M. tuberculosis are described.

Characterization, crystallization and preliminary X-ray crystallographic analysis of the human Uba5 C-terminus–Ufc1 complex

The human Uba5 C-terminal domain was demonstrated to be necessary for formation of the Ufc1–Ufm1 complex, and the minimal region for Ufc1 recognition was identified. The fusion protein between Uba5 381–404 and Ufc1 was expressed, purified and crystallized, and diffraction data were collected to 3.0 Å resolution.

Crystallization and preliminary X-ray analysis of a ribokinase from Vibrio cholerae O395

A ribokinase from V. cholerae O395 has been cloned, overexpressed, purified and crystallized both in a native form and in a ribose- and ADP-bound form. Both crystals belonged to space group P1. Apo crystals of ribokinase diffracted to 3.4 Å resolution and the co-crystals diffracted to 1.75 Å resolution.

Crystallographic characterization of the C-terminal coiled-coil region of mouse Bicaudal-D1 (BICD1)

The C-terminal coiled-coil (CC3) region of mouse Bicaudal-D1 (BICD1) and its complex with the small GTPase Rab6 were purified and crystallized. Crystals of the BICD1 CC3 region alone were obtained, but not of the BICD1–Rab6 complex, and X-ray diffraction data were collected from the BICD1 CC3 crystals to a resolution of 1.50 Å for phase determination by the multi-wavelength anomalous dispersion method.

Protein crystallization with microseed matrix screening: application to human germline antibody Fabs

The power of microseed matrix screening is demonstrated in the crystallization of a panel of antibody Fab fragments.