Enzyme Structure and Function

Active site tyrosine residues in human NQO1 homodimer are critical for non-synchronous enzyme catalysis at the two active sites.

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

High throughput protein serial crystallography using a grease matrix and a large-area support film

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: connecting deep generative models and crystallography

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

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Structural characterization of pyruvic oxime dioxygenase, a key enzyme of heterotrophic nitrification

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.

A glycerol oxidase from Norway spruce (Picea abies L. Karst.) expands biochemical and structural attributes of the GMC oxidoreductase superfamily

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

Scalable Fabrication of an Array-Type Fixed-Target Device for Automated Room Temperature X-ray Protein Crystallography

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

Ligand Identification in CryoEM and X-ray Maps Using Deep Learning

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.

Modeling Bias Toward Binding Sites in PDB Structural Models

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

I/σI vs {Rmerg, Rmeas, Rpim, CC1/2} for Crystal Diffraction Data Quality Evaluation

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.

Unveiling Mechanistic and Structural Insights of EstS1 Esterase: A Potent Broad-Spectrum Phthalate Diester Degrading Enzyme

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.

IspE Kinase as an Anti-infective Target: Role of a Hydrophobic Pocket in Inhibitor Binding

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.

Scaling and Merging Time-Resolved Laue Data with Variational Inference

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.

Structure of the turnover-ready state of an ancestral respiratory complex I

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.

Molecular insights into the oligosaccharide binding, recognition and hydrolysis by a fungal exo-beta-(1,3)-glucanase

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.

Crystal structure of a bacterial photoactivated adenylate cyclase determined at room temperature by serial femtosecond crystallography

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.

Expression, purification, and characterization of diacylated Lipo-YcjN from Escherichia coli

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

On the function of TRAP substrate-binding proteins: conformational variation of the sialic acid binding protein SiaP

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: Deep Learning Tools Trained on Protein Crystallisation Micrographs to Enable Automation of Experiments

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

Laue-DIALS: open-source software for polychromatic X-ray diffraction data

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.

Identifying novel chemical matter against the Chikungunya virus nsP3 macrodomain through crystallographic fragment screening

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

Structural Determinants of Vibrio cholerae FeoB Nucleotide Promiscuity

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

The nucleating agent crystallophore induces instant protein crystallization

This paper demonstrates how the crystallophore TbXo4 accelerates protein crystallization, enabling high-quality crystals for serial crystallography methods.

Metal fluorides - multi-functional tools for the study of phosphoryl transfer enzymes

The paper describes metal fluorides as tools for studying phosphoryl transfer enzymes, highlighting their use in structural biology techniques and introducing scandium tetrafluoride as a new analog.

In the AlphaFold era, when is experimental phasing of protein crystals still required?

The paper assesses how many protein structures still require experimental phasing when using AlphaFold 2 models, finding that most can be solved with Molecular Replacement.

Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron

This study uses mix-and-inject serial crystallography to resolve the catalytic mechanism of DJ-1, showing it catalyzes nearly two turnovers and reveals allosteric communication during glyoxalase activity.

Using deep learning predictions reveals a large number of register errors in PDB deposits

The paper identifies thousands of register errors in PDB structures using deep learning predictions and shows corrections improve refinement statistics.

Two-Metal Ion Mechanism of DNA Cleavage by Activated, Filamentous SgrAI

The paper presents two cryo-EM structures of filamentous SgrAI to elucidate the two-metal ion mechanism of DNA cleavage during enzymatic activity.

In-situ serial crystallography facilitates 96-well plate structuralanalysis at low symmetry

This paper introduces an in situ serial crystallography method for analyzing 96-well plates, enabling structure determination of challenging samples at low symmetry.

Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo

This study uses time-resolved crystallography to investigate the catalytic mechanism of His-Me family I-PpoI nuclease, revealing the role of a single divalent metal ion and histidine in DNA hydrolysis.