Newsletter

search results

results of search on CRYSTALLOGRAPHY JOURNALS ONLINE

22 citations found for Miyakawa,

Search for Miyakawa, in the World Directory of Crystallographers

Select bibliographic records for downloading using the checkboxes or select all button

Results 1 to 20, sorted by name:


Download citation
Download citation

link to html
asHPAL, a member of the HpaI/HpcH subfamily of class II aldolases, was expressed, purified and crystallized in the absence and presence of 2-ketobutyrate as one of its substrates using the sitting-drop vapour-diffusion method. asHPAL crystals grown without and with 2-ketobutyrate diffracted to 1.60 and 1.55 Å resolution, respectively.


Download citation
Download citation

link to html
The purification and crystallization of 3-quinuclidinone reductase from A. tumefaciens allowed the collection of a diffraction data set to 1.72 Å resolution.

Download citation
Acta Cryst A. (2013). A69, s304
Download citation


Download citation
Download citation

link to html
Primary and secondary extinction are studied using the dynamical theory of X-rays diffracted by imperfect crystals. The transition from dynamical to kinematical scattering is explained in terms of fundamental processes in diffraction. Contrary to existing extinction theories, where the intensities diffracted dynamically by single coherent domains of a mosaic are combined using an ad hoc assumption of mosaic distributions, the present theory permits the dynamical amplitudes to change in response to disturbances of the dynamical interactions by imperfections. Neither the mosaic block model nor the statistical treatment of imperfections is used. The extinction of diffracted intensities is thereby treated as caused solely by inhomogeneous strains in a single coherent domain.



Download citation
Download citation

link to html
Overexpression, purification and crystallization of the YjgF/YER057c/UK114-family protein from S. tokodaii strain 7 allowed the collection of a complete data set to 2.0 Å resolution.

Download citation
Download citation

link to html
Purification and crystallization of ginkbilobin-2 and its selenomethionine derivative allowed the collection of complete data to 2.38 Å resolution and multiwavelength anomalous diffraction data sets, respectively.

Download citation
Acta Cryst. (2014). A70, C213
Download citation

link to html
Restriction-modification systems consist of genes that encode a restriction enzyme and a cognate modification methyltransferase. It was believed that restriction enzymes are sequence-specific endonucleases that introduce double-strand breaks at specific sites by catalyzing the cleavages of phosphodiester bonds. R.PabI is a type II restriction enzyme from a hyperthermophilic archaea Pyrococcus abyssi that recognizes 5'-GTAC-3' sequence and cleaves DNA duplexes without the addition of a divalent cation. The structural and mutational analyses of R.PabI in our previous work showed that R.PabI forms a homodimer and has a novel DNA-binding fold called a "half-pipe," which consists of a highly curved anti-parallel [beta]-sheet. Because the structure of R.PabI shares no structural similarity to any other protein, the structural basis of the sequence-recognition and DNA-cleavage mechanisms remained unclear. In this study, we report the crystal structure of R.PabI in complex with a DNA duplex containing the R.PabI recognition sequence. The structure of the R.PabI-DNA complex shows that R.PabI unwinds a DNA duplex at a 5'-GTAC-3' site and flips the guanine and adenine bases out of the DNA helix to recognize the sequence. The electron-density map of the R.PabI-DNA complex shows that R.PabI releases adenine bases from the R.PabI recognition sequence. Biochemical assays using HPLC and MALDI-TOF MS spectrometry also support the observation that R.PabI releases adenine bases by hydrolysis. These results show that R.PabI is not an endonuclease but a sequence-specific adenine DNA glycosylase. R.PabI is the first example of a restriction enzyme that shows DNA glycosylase activity. Mutational analysis reveals the active site of the adenine DNA glycosylase activity of R.PabI. The two opposing apurinic/apyrimidinic (AP) sites generated by R.PabI are cleaved by heat promoted [beta] elimination and/or by endogenous AP endonucleases of host cells to introduce a double-strand break.


Download citation
Download citation

link to html
The crystal structures of A. jandaei L-allo-threonine aldolase and a mutant were refined to 2.59 and 2.50 Å resolution, respectively. The structural basis of the substrate specificity and stereoselectivity has been elucidated.

Download citation
Download citation


Download citation
Download citation

link to html
An RNA aptamer in complex with the human IgG Fc fragment have been crystallized. The stirring technique with a rotary shaker was used to improve the crystals and to ensure that they were of high quality and single, resulting in crystals that diffracted to 2.2 Å resolution.


Download citation
Download citation

link to html
Carbonyl reductase S1 from C. magnoliae was expressed, purified and crystallized. The crystals obtained diffracted X-rays to 1.90 Å resolution and belonged to space group P6122 or P6522.

Download citation
Download citation

link to html
The NADPH-dependent 3-quinuclidinone reductase from Rhodotorula rubra was expressed, purified, and crystallized and X-ray diffraction data of this crystal were collected to 2.2 Å resolution.


Download citation
Acta Cryst. (2014). A70, C1062
Download citation

link to html
The terpenoid, small-compound strigolactones (SLs) are plant hormones that regulate plant shoot branching, which is an important agronomic trait that determines crop yields. An [alpha]/[beta]-hydrolase protein, DWARF14 (D14), has been recognized to be an essential component of plant SL signaling. Recently, it has been demonstrated that D14 interacts with a gibberellin (GA)-signaling repressor SLR1 in an SL-dependent manner [1], which suggests that SLR1 mediates crosstalk between the SL and GA signalings in the regulation of plant shoot branching. Although D14 functions in SL perception to promote the interaction with SLR1, its molecular mechanism remains unclear. Here, we report the crystal structure of D14 in the complex with 5-hydroxy-3-methylbutenolide (D-OH), which is a reaction product of SLs. The structure was solved at a 2.10-Å resolution when an SL synthetic analogue, (-)-ent-2'-epi-GR7, was soaked into D14 crystals [1]. In the complex structure, D-OH was located at a site far from the catalytic residues including H297 and appeared to function as a plug for the catalytic cavity to induce an overall hydrophobic surface with a hydrophilic patch between the two [alpha]-helices in the cap structure of D14. In the binding site, the indole amine of Trp205 formed a hydrogen bond with the oxygen atom of the C2' hydroxy group, which arose from the catalytic reaction of D14, instead of a water molecule in the structure of apo D14. In addition, the side chain of Phe245 moved 1.3 Å toward D-OH. Mutational analyses of D14 showed that the interaction between D14 and SLR1 required an enzymatic activity of D14 and the residues Trp205 and Phe245 were essential for the SL-dependent SLR1-binding of D14. These results suggest that the D14-D-OH complex mediates the interaction with SLR1 in which the D-OH-induced surface and/or structural change is crucial.

Download citation
Download citation

link to html
Dioscorin from D. japonica was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. The dioscorin crystal diffracted X-rays to 2.11 Å resolution.

Follow IUCr Journals
Sign up for e-alerts
Follow IUCr on Twitter
Follow us on facebook
Sign up for RSS feeds