Diffraction structural biology – a new horizon

An introductory overview to the special issue papers on diffraction structural biology in this issue of the journal.

Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam

The development of a high-duty-cycle microsecond time-resolution SAXS capability at the Biophysics Collaborative Access Team beamline (BioCAT) 18ID at the Advanced Photon Source, Argonne National Laboratory, USA, is reported.

Cryo-electron tomography: moving towards revealing the viral life cycle of Rice dwarf virus

The viral and virus-related structures of Rice dwarf virus have been visualized by cryo-electron microscopy and tomography revealing the viral infection and replication mechanisms.

U-shape rotating anti-cathode compact X-ray generator: 20 times stronger than the commercially available X-ray source

A new type of U-shape anti-cathode X-ray generator in which the inner surface of a cylindrical target is irradiated by an electron beam has been made by modifying a conventional rotating anti-cathode X-ray generator whose brightness in the catalog is 12 kW mm⁻². A brightness of 129 kW mm⁻² was thereby obtained with this new U-shape-type X-ray generator. This new X-ray generator is expected to be of keen interest for applications in academia, industry and in hospitals.

Hydrogen-bond network and pH sensitivity in human transthyretin

The neutron crystal structure of human transthyretin is presented.

New methodologies at PF AR-NW12A: the implementation of high-pressure macromolecular crystallography

The evolution of AR-NW12A into a multi-purpose end-station with optional high-pressure crystallography is described.

Structural studies of haemoglobin from pisces species shortfin mako shark (Isurus oxyrinchus) at 1.9 Å resolution

Shortfin mako shark haemoglobin adopts an unliganded deoxy T state conformation, which is shown from the quaternary structural features, interface interactions and heme binding sites of different subunits of haemoglobin with high-resolution X-ray data.

Morphological image processing for qu­antitative shape analysis of biomedical structures: effective contrast enhancement

A contrast enhancement approach utilizing a new type of mathematical morphology called rotational morphological processing is introduced. The method is quantitatively evaluated and then applied to some medical images.

Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation

Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution.

Phase-diagram-guided method for growth of a large crystal of glycoside hydrolase family 45 inverting cellulase suitable for neutron structural analysis

The crystallization-phase-diagram-guided method is effective for growing large protein crystals for neutron protein crystallography.

Structural fluctuation observed in Z-DNA d(CGCGCG)₂ in the absence of divalent metal cations and polyamines

Various structural fluctuations of phosphate groups and hydration in the minor groove were observed in the crystal structure of Z-DNA in the absence of divalent metal cations and polyamines.

Structure of liposome encapsulating proteins characterized by X-ray scattering and shell-modeling

Wide-angle X-ray scattering data using a third-generation synchrotron radiation source are presented.

X-ray structure determination and deuteration of nattokinase

X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis.

Experiences with archived raw diffraction images data: capturing cisplatin after chemical conversion of carboplatin in high salt conditions for a protein crystal

Archiving of raw diffraction images data has led to new structural chemistry information being obtained for previously published results, which leads to the conclusion that carboplatin has partially converted to cisplatin in the high NaCl concentration conditions used in the crystallization procedure.

Crystal structure of endo-1,4-β-glucanase from Eisenia fetida

The crystal structure of endo-1,4-β-glucanase from the earthworm Eisenia fetida, which retained sufficient cellulase activity at low temperature, was determined at 1.5 Å resolution.

Improvement of an automated protein crystal exchange system PAM for high-throughput data collection

A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed.

Crystal structure of UDP-glucose:anthocyanidin 3-O-glu­cosyltransferase from Clitoria ternatea

The anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea (Ct3GT-A) was expressed in Escherichia coli, and the three-dimensional structure of Ct3GT-A was determined using X-ray crystallography. This report describes the architecture of Ct3GT-A, including the structures of the donor- and acceptor-binding sites.

High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging

A code with an algorithm for high-speed classification of X-ray diffraction patterns has been developed. Results obtained for a set of 1 × 10⁶ simulated diffraction patterns are also reported.

Crystal structure of human cyclin-dependent kinase-2 complex with MK2 inhibitor TEI-I01800: insight into the selectivity

The Gly-rich loop of cyclin-dependent kinase 2 (CDK2) bound to TEI-I01800 as an MK2 specific inhibitor forms a β-sheet which is a common structure in CDK2–ligand complexes. Here, the reason why TEI-I01800 does not become a strong inhibitor against CDK2 based on the conformation of TEI-I01800 is presented.

SPring-8 BL41XU, a high-flux macromolecular crystallography beamline

SPring-8 BL41XU provides a high-flux X-ray beam of size 10–50 µm, and enables high-quality diffraction data to be obtained from various types of protein crystals. Details of this beamline and an upgrade project are described.

Crystal structure of a complex of human chymase with its benzimidazole derived inhibitor

The crystal structure of human chymase complexed with a novel benzimidazole inhibitor, TJK002, was determined at 2.8 Å resolution. The present study shows that the benzimidazole ring of the inhibitor takes the stable stacking interaction with the protonated His57 in the catalytic domain of human chymase.

Modulation of the intermolecular interaction of myoglobin by removal of the heme

The present study analysed small-angle X-ray scattering profiles of myoglobin to examine how removal of the heme changes the intermolecular interaction.

Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilino­naphthalene-8-sulphonic acid

The crystal structure of human-heart-type fatty-acid-binding protein in complex with anilinonaphthalene-8-sulfonate was solved at 2.15 Å resolution revealing the detailed binding mechanism of the fluorescent probe 1-anilinonaphthalene-8-sulfonate.

A docking study of enhanced intracellular survival protein from Mycobacterium tuberculosis with human DUSP16/MKP-7

A docking study of Mtb Eis with its substrate DUSP16/MKP-7 was performed. The docking model suggests dissociation of hexameric Mtb Eis into dimers or monomers.

Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease

According to the structural and biochemical analysis of the stomatin-specific protease 1510-N, two degraded products were produced via acyl-enzyme intermediates. The N-terminal half of the substrate peptide binds to 1510-N more tightly than the C-terminal half of the peptide.

Improvements toward highly accurate diffraction experiments at the macromolecular micro-crystallography beamline BL-17A

The BL-17A macromolecular crystallography beamline at the Photon Factory was updated to improve the accuracy of diffraction experiments conducted using tiny crystals.

Structure basis 1/2SLPI and porcine pancreas trypsin interaction

1/2SLPI is a C-terminal domain of SLPI (secretory leukocyte protease inhibitor) which inhibits various serine proteases broadly. The present study is the first X-ray structural report on how 1/2SLPI with P1 Leu strongly inhibits trypsin and how it can inhibit multiple serine proteases.

Development of an online UV–visible microspectrophotometer for a macromolecular crystallography beamline

An online UV–visible microspectrophotometer has been developed for the macromolecular crystallography beamline at SPring-8. Details of this spectrophotometer are reported.

Creation and structure determination of an artificial protein with three complete sequence repeats

An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry.

Fundamental studies for the proton polarization technique in neutron protein crystallography

Fundamental trials to realise the proton polarization technique for detecting hydrogen with higher sensitivity in neutron protein crystallography are described.

High-resolution crystal structure of Streptococcus pyogenes β-NAD⁺ glyco­hydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD⁺ glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules.

JAXA protein crystallization in space: ongoing improvements for growing high-quality crystals

The Japan Aerospace Exploration Agency's `high-quality protein crystal growth' project is introduced. If crystallization conditions were carefully fixed in ground-based experiments, high-quality protein crystals grew in microgravity in many experiments on the International Space Station, especially when a highly homogeneous protein sample and a viscous crystallization solution were employed.

Crystal structure of human CK2α at 1.06 Å resolution

The high-resolution crystal structure of the human CK2 catalytic subunit reveals the structural insights that probably promote drug discovery.

Real-time investigation of protein unfolding at an air–water interface at the 1 s time scale

Protein unfolding at an air–water interface is followed in real time by a recently developed simultaneous multiple-angle–wavelength-dispersive X-ray reflectometer with a time resolution of 1 s.

Crystal structure of the N-terminal domain of MinC dimerized via domain swapping

The crystal structure of EcoMinC_NTD dimerized via domain swapping was solved at 2.3 Å resolution. The present study suggests that EcoMinC dimerizes through both EcoMinC_NTD and EcoMinC_CTD.

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method

Using the high-pressure cryocooling method, the high-resolution X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. This is the first ultra-high-resolution structure obtained from a high-pressure cryocooled crystal.

Evaluation of performance for IBARAKI biological crystal diffractometer iBIX with new detectors

The time-of-flight neutron single-crystal diffractometer iBIX at the next-generation neutron source J-PARC has been upgraded and is available for user experiments on protein samples in particular. Neutron structure analysis of a standard protein sample was carried out in order to evaluate the performance of iBIX.

A convenient tool for gas derivatization using fine-needle capillary mounting for protein crystals

A convenient gas-derivatization tool for protein crystals is presented in combination with a fine-needle capillary and a gas-pressure regulator.

Numerical model of protein crystal growth in a diffusive field such as the microgravity environment

Numerical analysis of the concentration depletion zones in a transient state suggested that, in microgravity, protein crystals grow in a lower supersaturation and the impurity ratio decreases in the centre of the crystal.

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