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Preview: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography

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


Multi-position data collection and dynamic beam sizing: recent improvements to the automatic data-collection algorithms on MASSIF-1
Significant improvements in the sample location, characterization and data collection algorithms on the autonomous ESRF beamline MASSIF-1 are described. The workflows now include dynamic beam diameter adjustment and multi-position and multi-crystal data collections.

Crystal structure of pyrrolizidine alkaloid N-oxygenase from the grasshopper Zonocerus variegatus
The high-resolution crystal structure of a Zonocerus variegatus flavin-dependent monooxygenase is reported at 1.6 Å alongside with kinetic studies of structure-based protein variants to investigate significant differences in enzyme activity between isoforms.

Microfocus Diffraction from Different Regions of a Protein Crystal: Structural Variations and Unit Cell Polymorphism
Microfocus X-ray data collection from 18 non-overlapping regions of a single protein crystal reveals unit cell non-isomorphism and subtle protein dynamics across the crystal specimen.

Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment
New developments in the MrBUMP pipeline, including graphical interaction with search models using CCP4mg and the use of ensemble search models, are reported.

Phosphoramidon inhibits the integral membrane protein zinc metalloprotease ZMPSTE24
The interaction between the integral membrane protein zinc metalloprotease ZMPSTE24 and the natural product broad-specificity zinc metalloprotease peptidic inhibitor phosphoramidon has been characterized functionally and structurally. Our functional results demonstrate ZMPSTE24 sensitivity to phosphoramidon in a manner consistent with competitive inhibition, as in soluble zinc metalloproteases, and that phosphoramidon's overall mode of binding to ZMPSTE24 and soluble zinc metalloproteases, especially gluzincins, is conserved.

The crystal structure of Proteus vulgaris tryptophan indole-lyase complexed with oxindolyl-l-alanine: implications for the reaction mechanism
The structure of tryptophan indole-lyase with a bound inhibitor, oxindolyl-L-alanine, was determined. The structure provides new insights for the enzyme reaction mechanism.

Worldwide Protein Data Bank validation information: usage and trends
The use of validation metrics to rank macromolecular structures, as well as a web tool to investigate trends in and correlations between different properties and validation metrics, are described.

APE1 processing of AP sites with 5' mismatches
Mismatch conformations are dynamic and vary depending on the environment, including restraints imposed by DNA binding proteins such as APE1, a key DNA repair enzyme. Here, we highlight both key insights revealed by X-ray crystallography of APE1 bound to mismatch containing substrates and the specific challenges associated with elucidating base pairing properties based on implied protonation states and X-ray crystallography data alone.

Density and electron density of aqueous cryoprotectant solutions at cryogenic temperatures for optimized cryoprotection and diffraction contrast
The T = 77 K densities of aqueous solutions of eight common cryoprotectants are measured, and are used to determine T = 77 K electron densities and thermal contractions on cooling from room temperature. These results provide a quantitative basis for choosing cryoprotectants to optimize outcomes in cryocrystallography, cryo-SAXS, cryogenic temperature X-ray imaging and vitrification-based biological cryopreservation.

Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguity
A method is presented to simultaneously resolve the crystal symmetry and indexing ambiguity from sparse data sets.

Structural rearrangements occurring upon cofactor binding in the Mycobacterium smegmatis β-ketoacyl-acyl carrier protein reductase MabA
High-resolution crystal structures of closed and open conformations of M. smegmatis MabA are reported.

Bacteroides thetaiotaomicron generates diverse α-mannosidase activities through subtle evolution of a distal substrate-binding motif
Analysing two sequence-related bacterial CAZy family GH92 mannosidases with distinct function, a structural basis for their varied specificities is revealed.

Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition
Structures of native and variants (T84S and T84A) of M. tuberculosis class II fructose-1,6-bisphosphatase are presented and compared with those of other homologs. The structure is a 222-symmetric homotetramer. Citrate was bound at a dimer interface and was found to be an inhibitor.

The crystal structure of the malic enzyme from Candidatus Phytoplasma reveals the minimal structural determinants for a malic enzyme
The crystal structure of the malic enzyme from aster yellows witches'-broom (Candidatus Phytoplasma) is reported. The structure showcases a minimal scaffold harbouring malic enzyme activity, shedding light on the evolution of complex malic enzymes.

The complex analysis of X-ray mesh scans for macromolecular crystallography
A method and software program, MeshBest, for the detection of individual crystals based on two-dimensional X-ray mesh scans are presented.

Validation of ligands in macromolecular structures determined by X-ray crystallography
Better metrics are required to be able to assess small-molecule ligands in macromolecular structures in Worldwide Protein Data Bank validation reports. The local ligand density fit (LLDF) score currently used to assess ligand electron-density fit outliers produces a substantial number of false positives and false negatives.

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps
ISOLDE is an interactive molecular-dynamics environment for rebuilding models against experimental cryo-EM or crystallographic maps. Analysis of its results reinforces the need for great care when validating models built into low-resolution data.

Structural and functional roles of dynamically correlated residues in thymidylate kinase
Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of thymidylate kinase.

Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE
Novel ways to produce search models from distant homologues for molecular replacement are presented.

Fragon: rapid high-resolution structure determination from ideal protein fragments
A new pipeline to solve structures by molecular replacement with ideal protein fragments is described and benchmarked against two test sets of mixed α/β and all-β folds at relatively high resolution.

Microtubule architecture in vitro and in cells revealed by cryo-electron tomography
Electron microscopy is a key methodology for studying microtubule structure and organization. Here, the results of cryo-electron tomography experiments on in vitro polymerized microtubules and comparisons with microtubule ultrastructure in cells are described.

The crystal structure of the lipoaminopeptaibol helioferin, an antibiotic peptide from Mycogone rosea
The structure of the natural lipoaminopeptaibol helioferin is reported. It is a nonapeptide that contains only four proteinogenic amino-acid residues; two long aliphatic carbon chains protrude out from either side of the N-terminus of the helical peptide, giving rise to the corkscrew shape of the molecule.

Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis
The type III pullulan hydrolase from T. kodakarensis (TK-PUL) possesses both pullulanase and α-amylase activities and has many potential applications in the industrial food-processing sector. Here, the crystal structure of TK-PUL is reported, which represents the first type III pullulan hydrolase structure to be solved, revealing N-terminal and C-terminal domains with significant differences from homologous structures.

IMAGINE: neutrons reveal enzyme chemistry
The capabilities of the IMAGINE neutron protein diffractometer at the Oak Ridge National Laboratory High Flux Isotope Reactor and highlights of the first five years of the scientific program are reviewed.

X-ray and UV radiation-damage-induced phasing using synchrotron serial crystallography
Multi-crystal serial crystallography data can be used for UV and X-ray radiation-damage-induced phasing.

Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement
Maximum-likelihood rigid-body refinement can be carried out to improve oriented models before the translation-function step of molecular replacement.

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination
ARCIMBOLDO_SHREDDER solves structures using fragments from low-homology models. Search fragments are improved through refinement or trimming against the experimental data. Consistent solutions are combined.

Overview of refinement procedures within REFMAC5: utilizing data from different sources
Here, a macromolecule-centred approach to three-dimensional structure determination as implemented in REFMAC5 is considered. The use of restraints to transfer chemical and structural information during macromolecular refinement, and how different sources of information can be combined in order to achieve models that are more consistent with data derived from a variety of experimental techniques, including macromolecular crystallography, cryo-EM and NMR spectroscopy, are discussed.

ARCIMBOLDO on coiled coils
The ARCIMBOLDO method of phasing through the location of small fragments combined with density modification and autotracing is particularly suited to helical structures, but coiled coils remain challenging. Features designed for solving coiled coils at resolutions of up to 3 Å were tested on a pool of 150 structures.

DIALS: implementation and evaluation of a new integration package
A new X-ray diffraction data-analysis package is presented with a description of the algorithms and examples of its application to biological and chemical crystallography.

Where is crystallography going?
Macromolecular crystallography has provided results that underpin much biological discovery and there is still scope for further development; however, a revolution in electron imaging now means that it can also routinely provide detailed atomic-level descriptions. This article attempts to tease out where crystallography is going and consider what its place might be in the new landscape.

CCP4i2: the new graphical user interface to the CCP4 program suite
CCP4i2 is a graphical user interface to the CCP4 (Collaborative Computational Project, Number 4) software suite and a Python language framework for software automation.

An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features
Experimental phasing of macromolecular crystals is described and explained, with the emphasis on its implementation in the programs SHELXC, SHELXD and SHELXE, which are also used in a number of macromolecular structure-solution pipelines.

Distributed computing for macromolecular crystallography
The paper describes recent CCP4 initiatives and projects aimed at bringing software and data services which utilize distributed computational resources to users.

Substructure determination using phase-retrieval techniques
The relaxed averaged alternating reflections (RAAR) phase-retrieval method has been applied to crystallography for the first time and has been shown to outperform charge flipping in anomalous substructure determination.

Macromolecular refinement by model morphing using non-atomic parameterizations
A method is described for the refinement of an electron-density model against a set of structure-factor observations which does not rely on atomic parameters. The effective level of detail in the parameterization can be varied to ensure that the refinement is well determined at any resolution supported by the data.

Maximum-likelihood determination of anomalous substructures
Likelihood-based SAD substructure determination can be initiated using a fast translation-search algorithm based on a linear approximation to the SAD likelihood target, followed by log-likelihood-gradient map completion.

Model validation: local diagnosis, correction and when to quit
An overview is provided of current crystallographic model validation of proteins and RNA, both foundations and criteria, at all resolution ranges, together with advice on how to correct specific types of problems and when you should not try so hard that you are overfitting.