Enzyme Structure and Function

Unified access to up-to-date residue-level annotations from UniProt and other biological databases for PDB data via PDBx/mmCIF files

The paper integrates up-to-date residue-level annotations from multiple databases into PDBx/mmCIF files to improve data interoperability and standardization.

De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

The paper determines the structures of Cry11Aa and Cry11Ba toxins using serial femtosecond crystallography, revealing new insights into their in vivo crystallization patterns and toxicity.

PDB ProtVista: A reusable and open-source sequence feature viewer

PDB ProtVista is a sequence feature viewer that provides 2D visualization of residue-level annotations and integrates with 3D molecular viewers.

Structural analysis of 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding

The paper presents high-resolution crystal structures of DXPS from Pseudomonas aeruginosa and Klebsiella pneumoniae in different forms, revealing conformational changes upon cofactor binding and providing insights for drug design.

Slice'N'Dice: Maximising the value of predicted models for structural biologists

SliceNDice improves Molecular Replacement by splitting and repositioning predicted structural models to enhance accuracy in domain orientations.

Serial Crystallography with Multi-stage Merging of 1000s of Images

The paper introduces a multi-stage clustering strategy for serial crystallography data to improve dataset merging accuracy by first clustering based on unit cell parameters and then on reflection intensities.

xia2.multiplex: a multi-crystal data analysis pipeline

xia2.multiplex merges multi-crystal data sets in macromolecular crystallography to improve data quality and facilitate analysis.

MrParse: Finding homologues in the PDB and the EBI AlphaFold database for Molecular Replacement and more

MrParse streamlines Molecular Replacement by consolidating homologue searches and rankings from PDB and EBI AlphaFold, using eLLG and structural predictions.

A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs

The paper introduces a multi-factor clustering method to classify diffraction data from dynamic proteins into polymorphs, using unit cell constants and intensities to cluster mixed-state data from chymotrypsinogen crystals.

Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA

This paper identifies two drug-like fragments that bind to a cryptic pocket in B. pseudomallei DsbA, showing weak binding but potential for optimization.

Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

This study demonstrates a high-throughput drug screening protocol using serial femtosecond X-ray crystallography for SARS-CoV-2 main protease, achieving 120 images/second with a new detector.

A mosaic bulk-solvent model improves density maps and the fit between model and data

The paper introduces a mosaic bulk-solvent model that improves the fit between crystallographic models and data, enhancing density map quality and solving previously inaccessible problems.

Identification of unknown proteins in X-ray crystallography and cryo-EM

The paper presents an automated pipeline to identify protein sequences from cryo-EM and crystallographic data, demonstrating its application on an unknown snake venom protein.

Tunable hetero-assembly of a plant pseudoenzyme-enzyme complex

The paper investigates the tunable hetero-assembly of a plant pseudoenzyme-enzyme complex, revealing variable stoichiometry and structural insights into their interactions.

Assessing the utility of CASP14 models for molecular replacement

This paper evaluates CASP14 models for molecular replacement using a new metric, reLLG, which is independent of diffraction data and shows AlphaFold2 models outperform others.

Data and Diversity Driven Development of a Shotgun Crystallisation Screen using the Protein Data Bank

The paper develops a new protein crystallisation screen (Shotgun II) using PDB data, showing it outperforms the previous Shotgun I screen in coverage and data input.

PDBrenum: a webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences

PDBrenum renumbers PDB files to align with UniProt sequences, resolving inconsistent amino acid numbering across PDB entries.

Macromolecular refinement of X-ray and cryo-electron microscopy structures with Phenix / OPLS3e for improved structure and ligand quality

This paper improves macromolecular structure refinement using Phenix and OPLS3e for better structure and ligand quality in X-ray and cryo-EM data.

MCPdb: The Bacterial Microcompartment Database

The paper introduces MCPdb, a database cataloging bacterial microcompartment structures and their assemblies, annotated for assembly state, structure, and metabolic function.

Molecular basis for cysteine oxidation by Plant Cysteine Oxidases from Arabidopsis thaliana

The paper presents structures of Arabidopsis thaliana PCOs and identifies key residues for N-Cys oxidation, revealing substrate recognition and catalytic mechanisms.

Structural studies on M. tuberculosis decaprenyl phosphoryl-β-D-ribose epimerase-2 enzyme involved in cell wall biogenesis

This paper structurally characterizes MtbDprE2, an NADH-dependent enzyme in M. tuberculosis, and elucidates its NADH binding mechanism through circular dichroism, molecular modeling, and dynamics simulations.

Local and global analysis of macromolecular Atomic Displacement Parameters

This paper models macromolecular atomic displacement parameters using a mixture of Shifted Inverse Gamma Distributions and introduces a local analysis method for detecting structural errors.

Helical ensembles out-perform ideal helices in Molecular Replacement

This paper introduces helical ensembles as improved search models for molecular replacement, achieving a 30% increase in solutions and faster convergence compared to ideal helices.

A chemical interpretation of protein electron density maps in the worldwide protein data bank

The paper develops a method to convert electron density maps into units of electrons, enabling biochemical interpretation of structural quality in PDB entries.

Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes

The paper determines crystal structures of SARS-CoV-2 ADRP and shows conformational changes upon ligand binding, identifying a conserved water molecule involved in hydrolysis.

An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism

The paper identifies an iron-dependent enzyme in plants that completes the lysine catabolism pathway, showing structural and functional conservation across species.

An automated data processing and analysis pipeline for transmembrane proteins in detergent solutions

The paper introduces an automated pipeline for SAXS data analysis of transmembrane proteins in detergent solutions, improving model resolution with a priori information.

Model reconstruction from Small angle X-ray Scattering data using deep learning methods

The paper presents a deep learning algorithm using an auto-encoder to reconstruct 3D protein models from SAXS data, demonstrating accuracy without prior size information.

Obtaining tertiary protein structures by the ab-initio interpretation of small angle X-ray scattering data

This paper introduces an ab-initio method to derive 3D protein structures from SAXS data and primary sequences, validated using crystal structures and showing success in modeling a coiled-coil protein.

Including Crystallographic Symmetry in Quantum-based Refinement: Q|R#2

The paper refines a protein structure using quantum chemistry restraints, incorporating crystallographic symmetry effects through a fragmentation approach.