Subscribe: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography
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Forthcoming article in Acta Crystallographica Section D Structural Biology



Acta Crystallographica Section D: Structural Biology welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports o



 



Guidelines for successful generation of protein–ligand complex crystals
This article aims to guide efforts in protein-ligand complex crystal structure generation with special considerations on protein construct design, and summarizes different approaches to co-crystallization and crystal soaking. Common problems and pitfalls are highlighted.



Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry
H atoms are 'hard to see' in X-ray crystal structures of protein-ligand complexes. This paper discusses the problem of identifying the correct tautomeric form(s) of protein bound ligands.



The XChemExplorer graphical workflow tool for routine or large-scale protein–ligand structure determination
XChemExplorer (XCE) is a graphical workflow and data-management tool for the parallel determination of protein–ligand complexes. Its implementation, usage and application are described here.



Ligand fitting with CCP4
The process of ligand fitting with CCP4 is reviewed, including identifying ligand density in the map, ligand fitting, refinement and subsequent validation. Recent developments are discussed, and are illustrated using instructive examples demonstrating practical application.



Crystal structure of human chondroadherin: solving a difficult molecular-replacement problem using de novo models
The structure of human chondroadherin (hCHAD), a 359-amino-acid protein with 11 leucine-rich repeats, has been solved by molecular replacement using de novo models of a 195-residue segment and the AMPLE pipeline. This demonstrates that even a fairly large β-rich protein is tractable to solution using de novo modelling. The structure of the C-terminal domain of hCHAD reveals the conformation of a medically relevant peptide.



Q|R: quantum-based refinement
Quantum-based refinement software is being developed to refine biomacromolecules against crystallographic or cryo-electron microscopy data.



The structure of a calcium-dependent phosphoinositide-specific phospholipase C from Pseudomonas sp. 62186, the first from a Gram-negative bacterium
The structure of the calcium-dependent phosphoinositide-specific phospholipase C from Pseudomonas sp. 62186 is described, the first from a Gram-negative bacterium. Structure solution from a low-sequence-identity homology model is described in detail.



Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder
In the course of soaking experiments of lytic polysaccharide monooxygenase crystals with potential oligosaccharide ligands, local changes in crystal packing, various degrees of active-site disorder and binding of oligosaccharides at potential branching or surface binding sites were observed.



Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis
X-ray structures of the enzyme 5-aminolaevulinate dehydratase (ALAD) purified from human blood, as well as the recombinant human form and the ALAD from the hyperthermophilic archaeon P. calidifontis, are reported, together with the structure of E. coli ALAD co-crystallized with a noncovalently bound moiety of the product, porphobilinogen. The structures give insight into the zinc-dependence of these enzymes, the possible role of electrostatics in substrate funnelling and details of the interactions made by the bound pyrrole end product.



Solution of the structure of a calmodulin–peptide complex in a novel configuration from a variably twinned data set
A description is given of the structure solution of a nearly perfectly hemihedrally twinned novel calmodulin–peptide complex by molecular replacement in combination with single-wavelength anomalous diffraction. The resulting structure revealed a unique mode of peptide–calmodulin interaction in which the peptide is bent to nearly 90° within the calmodulin-binding pocket.



A pipeline approach to single-particle processing in RELION
The formal description of a workflow to cryo-EM structure determination in the RELION program allows standardization of procedures and on-the-fly image processing during data acquisition.



Polder maps: improving OMIT maps by excluding bulk solvent
Residual OMIT maps can be improved by the selective exclusion of bulk solvent from the OMIT region.



Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core
A crystal structure of the U6 snRNP core from yeast shows that mutation of the U6 internal stem-loop (ISL) does not alter the overall topology of the snRNP, but suggests structural plasticity in the ISL.



Keep it together: restraints in crystallographic refinement of macromolecule–ligand complexes
An overview of the process of ligand restraint generation for macromolecular crystallographic refinement is given.



Strategies for carbohydrate model building, refinement and validation
This article addresses many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.



An editor for the generation and customization of geometry restraints
Obtaining a restraint dictionary for novel ligands or improving restraints for known ligands can require their manual modification. This can be tedious and error-prone. REEL is a restraints editor that provides quick, easy and accurate development, allowing global changes and fine-tuning of individual restraints.



Combining X-ray and neutron crystallography with spectroscopy
The use of neutron crystallography and in situ spectroscopy to study enzyme mechanism is discussed.



Twilight reloaded: the peptide experience
The potential causes of the severe misinterpretation of peptide density in a significant number of protein–peptide complex structures are analyzed, together with suggestions for good practice and specific education aimed at minimizing overinterpretation and mistakes in protein–peptide complex structure models.



Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis
A guide to how the Cambridge Structural Database can be used to aid macromolecular crystallography.