forthcoming articles in Acta Crystallographica Section D

The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Biological Crystallography.

See also Forthcoming articles in all IUCr journals.

Development of a Thermofluor assay for stability determination of membrane proteins using the Na⁺/H⁺ antiporter NhaA and cytochrome c oxidase

M. Kohlstaedt, I. von der Hocht, F. Hilbers, Y. Thielmann and H. Michel

Synopsis: The use of the thermofluor assay for membrane proteins is explored by testing five different detergents with common fluorescent probes. The dye 1-anilinonaphthalene-8-sulfonic acid is identified as a valuable tool when working with detergents and the membrane protein NhaA.

Structural insight into the thermostable NADP⁺-dependent meso-di­aminopimelate de­hydrogenase from Ureibacillus thermosphaericus

H. Akita, T. Seto, T. Ohshima and H. Sakuraba

Synopsis: The unique structure of thermostable meso-diaminopimelate dehydrogenase from Ureibacillus thermosphaericus was determined and compared with those of corresponding enzymes from other sources.

Structures of the Middle East respiratory syndrome coronavirus 3 C-like protease reveal insights into substrate specificity

D. Needle, G. T. Lountos and D. S. Waugh

Synopsis: MERS-CoV 3 CL^pro has been crystallized and X-ray crystal structures have been solved in three different crystal forms representing the free enzyme structure and enzyme-product complex.

Structures of Bacteroides fragilis uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (BfLpxA)

A. Ngo, K. T. Fong, D. L. Cox, X. Chen and A. Fisher

Synopsis: Bacteroides fragilis UDP-N-acetylglucosamine acyltransferase (BfLpxA) ligand free and UDP-N-acetylglucosamine-bound crystal structures

Against the odds? De novo structure determination of a pilin with two cysteine residues by sulfur SAD

M. Gorgel, A. Bøggild, J. J. Ulstrup, M. S. Weiss, U. Müller, P. Nissen and T. Boesen

Identification of local variations within secondary structures of proteins

P. Kumar and M. Bansal

Synopsis: ASSP is a freely available algorithm for secondary structure assignment in Protein structures. The algorithm is an extension of HELANAL-Plus and can be accessed at http://nucleix.mbu.iisc.ernet.in/assp/index.html.

REdiii: a pipeline for automated structure solution

M.-F. Bohn and C. A. Schiffer

Synopsis: The software pipeline REdiii allows fully automated crystal structure solution by embedding existing tools into a self-managing workflow.

Structural study of the X-ray-induced enzymatic reaction of octahaem cytochrome c nitrite reductase

A. A. Trofimov, K. M. Polyakov, V. A. Lazarenko, A. N. Popov, T. V. Tikhonova, A. V. Tikhonov and V. O. Popov

Synopsis: X-ray induced substrate (nitrite and sulfite) transformations are studied for cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens.

Structures of the hydrolase domain of zebrafish 10-formyltetra­hydrofolate de­hydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition

C.-C. Lin, P. Chuankhayan, W.-N. Chang, T.-T. Kao, H.-H. Guan, H.-K. Fun, A. Nakagawa, T.-F. Fu and C.-J. Chen

Synopsis: Structure of hydrolase domain of 10-formyltetrahydrofolate dehydrogenase from zebrafish and its complexes.

The role of monovalent cations in the ATPase reaction of DNA gyrase

S. J. Hearnshaw, T.T.-H. Chung, C. E. M. Stevenson, A. Maxwell and D. M. Lawson

Synopsis: New structures of the N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit reveal two discrete monovalent cation-binding sites that could have functional roles.

Structure of ginseng major latex-like protein 151 and its proposed lysophosphatidic acid-binding mechanism

S.-H. Choi, M.-K. Hong, H.-J. Kim, N. Ryoo, H. Rhim, S.-Y. Nah and L.-W. Kang

Synopsis: The crystal structure of GLP, its recognition of LPA, and the activation of G protein-coupled LPA receptor in complex with LPA.

Ambiguity assessment of small-angle scattering curves from monodisperse systems

M. V. Petoukhov and D. I. Svergun

Synopsis: A method is presented to quantitatively assess the inherent ambiguity of three-dimensional shape reconstruction from a given small-angle scattering pattern.

Combination of X-ray crystallography, SAXS and DEER to obtain the structure of FnIII-3,4 domains of integrin 64

N. Alonso-García, I. García-Rubio, J. A. Manso, R. M. Buey, H. Urien, A. Sonnenberg, G. Jeschke and J. M. de Pereda

Synopsis: The structure of the FnIII-3,4 region of the integrin 4 was solved using a hybrid approach that combines crystallographic structures, SAXS, DEER, and molecular modeling. The structure helps to understand how 4 might bind to other hemidesmosomal proteins and mediate signaling.

Structural and functional characterization of TesB from Yersinia pestis reveals a unique octameric arrangement of hotdog domains

C. M. D. Swarbrick, M. E. Perugini, N. Cowieson and J. K. Forwood

Synopsis: The structural and functional characterization of the tesB thioesterase from Yersinia pestis reveals unique elements within the protomer and quaternary arrangements of hotdog domains, presenting distinguishing features of this enzyme family.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis

B. Zarychta, A. Lyubimov, M. Ahmed, P. Munshi, B. Guillot, A. Vrielink and C. Jelsch

Synopsis: The hydrogen bonds stereochemistry and topology of the flavoenzyme cholesterol oxidase crystal structure are analyzed at the 0.94 Å optical resolution.

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

A. Y. Lyubimov, T. D. Murray, A. Koehl, I. E. Araci, M. Uervirojnangkoorn, O. B. Zeldin, A. E. Cohen, S. M. Soltis, E. L. Baxter, A. S. Brewster, N. K. Sauter, A. T. Brunger and J. M. Berger

Synopsis: A microfluidic platform has been developed for the capture and X-ray analysis of protein microcrystals, affording a means to improve the efficiency of XFEL and synchrotron experiments.

Time-lapse, anomalous X-ray diffraction shows how Fe²⁺ substrate ions move through ferritin protein nanocages to oxidoreductase sites

C. Pozzi, F. Di Pisa, D. Lalli, C. Rosa, E. Theil, P. Turano and S. Mangani

Synopsis: A series of high-resolution crystal structures of Rana catesbeiana ferritin M, loaded with Fe²⁺ substrate at different metal ion diffusion times, show a sequence of iron binding sites that allow visualize a possible path of substrate diffusion to the catalytic center.

Structures of complexes of type 5 17-hydroxysteroid de­hydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding

Y. Amano, T. Yamaguchi, T. Niimi and H. Sakashita

Synopsis: Crystal structures of type 5 17-hydroxysteroid dehydrogenase complexes with structurally diverse inhibitors reveal novel scaffolds and conformational changes.

Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase

M. Thomsen, A. Tuukkanen, J. Dickerhoff, G. J. Palm, H. Kratzat, D. I. Svergun, K. Weisz, U. T. Bornscheuer and W. Hinrichs

Synopsis: Elucidation of the first bacterial chalcone isomerase as native and substrate-bound crystal structures reveals structural homology to a chlorite dismutase, but no structural relation to a plant chalcone isomerase, suggesting a different evolutionary history. The catalytic site of the bacterial isomerase depends on a histidine side chain, in contrast to the catalytic water molecule of the plant enzyme.

Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization

J. L. Johnson, K. C. Entzminger, J. Hyun, S. Kalyoncu, D. P. Heaner, I. A. Morales, A. Sheppard, J. C. Gumbart, J. A. Maynard and R. L. Lieberman

Synopsis: A Fab fragment with nanomolar affinity for the peptide sequence EYMPME was engineered and characterized by structural, biophysical and computational methods for potential use as a membrane-protein crystallization chaperone.

Structure of the adenylation-peptidyl carrier protein didomain of the Microcystis aeruginosa microcystin synthetase McyG

X.-F. Tan, Y.-N. Dai, K. Zhou, Y.-L. Jiang, Y.-M. Ren, Y. Chen and C.-Z. Zhou

Synopsis: The first structure of an A-PCP didomain in which the A domain is in the adenylated state complexed with the intermediate L-Phe-AMP is described.

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

A. E. Langkilde, K. L. Morris, L. C. Serpell, D. I. Svergun and B. Vestergaard

Synopsis: The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained.

A covalent adduct of MbtN, an acyl-ACP de­hydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket

A.-F. Chai, E. M. M. Bulloch, G. L. Evans, J. S. Lott, E. N. Baker and J. M. Johnston

Synopsis: The structure of MbtN (Rv1346) presented here supports its annotation as the double-bond-forming dehydrogenase involved in the biosynthesis of mycobactin T in M. tuberculosis and reveals a novel FAD-PEG covalent adduct bound in a unique acyl-binding cavity.

Elucidation of the crystal structure of Coriolopsis caperata laccase: restoration of the structure and activity of the native enzyme from the T2-depleted form by copper ions

O. A. Glazunova, K. M. Polyakov, T. V. Fedorova, P. V. Dorovatovsky and O. V. Koroleva

Structure of the N-terminal domain of the protein Expansion: an `Expansion' to the Smad MH2 fold

M. Beich-Frandsen, E. Aragón, M. Llimargas, J. Benach, A. Riera, J. Pous and M. J. Macias

Synopsis: Expansion is a modular protein that is conserved in protostomes. The first structure of the N-terminal domain of Expansion has been determined at 1.6 Å resolution and the new N-MH2 domain was found to belong to the Smad/FHA superfamily of structures.

ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning

J. Sliwiak, Z. Dauter, M. Kowiel, A. J. McCoy, R. J. Read and M. Jaskolski

Synopsis: Hyp-1, a pathogenesis-related class 10 (PR-10) protein from H. perforatum, was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The asymmetric unit of the tetartohedrally twinned crystal contains 28 copies of the protein arranged in columns with noncrystallographic sevenfold translational symmetry and with additional pseudotetragonal rotational NCS.

Novel crystalline phase and first-order phase transitions of human insulin complexed with two distinct phenol derivatives

A. Valmas, K. Magiouf, S. Fili, M. Norrman, G. Schluckebier, D. Beckers, T. Degen, J. Wright, A. Fitch, F. Gozzo, A. E. Giannopoulou, F. Karavassili and I. Margiolaki

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains

Z. Wang, Z. Qiao, S. Ye and R. Zhang

The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation

Z. Yurtsever, S. M. Scheaffer, A. D. Romero, M. J. Holtzman and T. J. Brett

Structure of Arabidopsis thaliana Rubisco activase

D. Hasse, A. M. Larsson and I. Andersson

Synopsis: The crystal structure of Rubisco activase from A. thaliana is presented. The structure shows a high degree of conformational flexibility and indicates that subtle structural differences may influence interactions in the oligomeric complexes of green-type Rubisco activases.

Structure of stru­thiocalcin-1, an intramineral protein from Stru­thio camelus eggshell, in two crystal forms

R. R. Ruiz-Arellano, F. J. Medrano, A. Moreno and A. Romero

Synopsis: The crystal structure of struthiocalcin-1 (SCA-1) from ostrich eggshell has been determined in two different crystal forms at 1.50 Å resolution, displaying the characteristic C-type lectin-like fold with a surface decorated with acidic residues, highlighting the overall negative charge of SCA-1.

Radiation decay of thaumatin crystals at three X-ray energies

D. Liebschner, G. Rosenbaum, M. Dauter and Z. Dauter

Synopsis: A series of diffraction images of thaumatin crystals at identical small, 2° rotation intervals were recorded at three different X-ray energies (6.33, 12.66 and 19.0 keV) using five crystals at each energy. The decay in the average diffraction intensities at 100 K owing to radiation damage was analyzed and the dose that diminished the reflection intensities to 70% was determined to be about 7.5 MGy at 6.33 keV and about 11 MGy at the two higher energies.

A noncanonical PWI domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein

E. Absmeier, L. Rosenberger, L. Apelt, C. Becke, K. F. Santos, U. Stelzl and M. C. Wahl

Synopsis: A crystal structure and biochemical analyses reveal the presence of a PWI-like domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein, which does not stably bind nucleic acids but instead constitutes part of a protein-protein interaction region that binds several spliceosomal proteins in a yeast two-hybrid assay.

Structure of N-myristoyltransferase from Aspergillus fumigatus

T. Shimada, M. Suzuki and S.- Katakura

High-pressure protein crystallography of hen egg-white lysozyme

H. Yamada, T. Nagae and N. Watanabe

Synopsis: The crystal structure of hen egg-white lysozyme (HEWL) was analyzed under pressures of up to 950 MPa. The high pressure modified the conformation of the molecule and induced a novel phase transition in the tetragonal crystal of HEWL.

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