Enzyme Structure and Function

PDBCleanV2 generates consistent structure datasets by standardizing labeling, chain names, and numbering for protein structures.

The paper evaluates lossy compression methods for high data rate macromolecular crystallography to minimize information loss while maintaining structural analysis quality.

This study produces, purifies, and crystallizes 24C-sterol methyltransferase from Candida albicans to support future crystallographic studies.

This study reports three high-resolution structures of a broad-spectrum LarA enzyme, revealing substrate binding mode and residues critical for substrate recognition and catalysis.

This study investigates the role of Tyr126 and Tyr128 in human NQO1 catalysis, showing their critical impact on enzyme activity and non-synchronous catalysis.

The paper introduces a new method for high-throughput protein serial crystallography using a grease matrix and a large-area support film to improve efficiency and reduce sample consumption.

SFCalculator connects deep generative models with crystallography by generating crystallographic observables from molecular structures, enabling better integration of experimental data and machine learning.

This study determines the crystal structure of pyruvic oxime dioxygenase (POD) from Alcaligenes faecalis, revealing its catalytic mechanism and structural features involved in heterotrophic nitrification.

The paper characterizes PaAOX1, a plant AA3 oxidase from Norway spruce, revealing its unique biochemical activity and structural features within the GMC oxidoreductase superfamily.

This paper describes a scalable microfluidic device for automated X-ray crystallography that enables efficient and damage-free crystal mounting for protein structure analysis.

This study investigates the redox regulation of Mycobacterium tuberculosis cytochrome bd by its disulfide bond and quinone specificity, showing reduced activity upon disulfide reduction and substrate inhibition with menaquinol.

The paper introduces a deep learning method for ligand identification in cryoEM and X-ray density maps, showing it performs as well as existing methods for X-ray data and can be applied to cryoEM data.

The paper identifies that small molecule binding sites in PDB structural models are more accurately modeled than other regions, affecting structural interpretation and applications.

The paper evaluates crystal diffraction data quality metrics, finding that low-shell values of Rmerg, Rmeas, Rpim, and CC1/2 indicate Laue symmetry correctness, while high-shell I/σI is better for resolution cutoff selection.

This study introduces AXSI for measuring absolute intramolecular distances in proteins, validated against single-molecule FRET, showing its effectiveness under various solution conditions.

This study characterizes the structural and mechanistic properties of EstS1 esterase, revealing its role in degrading phthalate diesters through a bi-bi ping-pong mechanism and covalent substrate binding.

The paper identifies 38 cases of enzymes with different structures but identical functions, analyzing their sequence, structure, and mechanism to support convergent evolution.

The paper investigates IspE kinase homologs from pathogenic bacteria, identifies structural differences affecting inhibitor binding, and highlights a hydrophobic pocket critical for inhibitor specificity in Acinetobacter baumannii.

This paper applies variational inference to time-resolved diffraction data of an enzyme to extract high signal-to-noise changes in electron density and evaluates hyperparameter impact.

The paper presents the structure of respiratory complex I from Paracoccus denitrificans in a turnover-ready state, revealing elements stabilizing the closed state and its relevance to mammalian complex I.

This study characterizes the structure and function of Aspergillus oryzae exo-β-(1,3)-glucanase, revealing substrate binding mechanisms and insights for industrial enzyme engineering.

The paper determines the crystal structure of a bacterial photoactivated adenylate cyclase at room temperature using serial femtosecond crystallography and compares it with cryo structures to study structural changes upon light exposure.

This study determines the crystal structure of YcjN from E. coli, identifies its posttranslational diacylation, and explores its aggregation properties in solution.

This study solves the structure of the TRAP substrate-binding protein AaSiaP in different conformations, revealing how it binds N-acetylneuraminate and stabilizes a closed state.

CHiMP tools automate protein crystallisation experiments by classifying micrographs and detecting crystals and droplets using deep learning.

Laue-DIALS is an open-source software pipeline for analyzing polychromatic X-ray diffraction data, enabling efficient processing and integration of diffraction intensities with wavelength correction.

This study determines the cryoEM structures of human PFK1 in R- and T-states, revealing eukaryotic allosteric regulation mechanisms and the role of the C-terminus in autoinhibition.

The paper identifies chemical fragments targeting the Chikungunya virus nsP3 macrodomain through crystallographic screening, revealing novel binding sites and potential inhibitors.

This study identifies structural determinants of FeoB nucleotide promiscuity in Vibrio cholerae by analyzing crystal structures and thermodynamics.