Literature DB >> 27917838

Overcoming a hemihedral twinning problem in tetrahydrofolate-dependent O-demethylase crystals by the microseeding method.

Ayaka Harada1, Yukari Sato2, Naofumi Kamimura3, Nagarajan Venugopalan4, Eiji Masai3, Toshiya Senda1.   

Abstract

A tetrahydrofolate-dependent O-demethylase, LigM, from Sphingobium sp. SYK-6 was crystallized by the hanging-drop vapour-diffusion method. However, the obtained P3121 or P3221 crystals, which diffracted to 2.5-3.3 Å resolution, were hemihedrally twinned. To overcome the twinning problem, microseeding using P3121/P3221 crystals as microseeds was performed with optimization of the reservoir conditions. As a result, another crystal form was obtained. The newly obtained crystal diffracted to 2.5-3.0 Å resolution and belonged to space group P21212, with unit-cell parameters a = 102.0, b = 117.3, c = 128.1 Å. The P21212 crystals diffracted to better than 2.0 Å resolution after optimizing the cryoconditions. Phasing using the single anomalous diffraction method was successful at 3.0 Å resolution with a Pt-derivative crystal. This experience suggested that microseeding is an effective method to overcome the twinning problem, even when twinned crystals are utilized as microseeds.

Entities:  

Keywords:  O-demethylase; Sphingobium sp. SYK-6; cryoprotectant; hemihedral twinning; microseeding; tetrahydrofolate

Mesh:

Substances:

Year:  2016        PMID: 27917838      PMCID: PMC5137467          DOI: 10.1107/S2053230X16018665

Source DB:  PubMed          Journal:  Acta Crystallogr F Struct Biol Commun        ISSN: 2053-230X            Impact factor:   1.056


  24 in total

1.  A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning.

Authors:  Jennifer E Padilla; Todd O Yeates
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2003-06-27

2.  Detecting and overcoming crystal twinning.

Authors:  T O Yeates
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

3.  Solvent content of protein crystals.

Authors:  B W Matthews
Journal:  J Mol Biol       Date:  1968-04-28       Impact factor: 5.469

4.  Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls.

Authors:  Eiji Masai; Naofumi Kamimura; Daisuke Kasai; Akio Oguchi; Akiho Ankai; Shigehiro Fukui; Mikio Takahashi; Isao Yashiro; Hiroki Sasaki; Takeshi Harada; Sanae Nakamura; Yoko Katano; Sachiko Narita-Yamada; Hidekazu Nakazawa; Hirofumi Hara; Yoshihiro Katayama; Masao Fukuda; Shuji Yamazaki; Nobuyuki Fujita
Journal:  J Bacteriol       Date:  2012-01       Impact factor: 3.490

5.  A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate.

Authors:  Eiji Masai; Miyuki Sasaki; Yasunori Minakawa; Tomokuni Abe; Tomonori Sonoki; Keisuke Miyauchi; Yoshihiro Katayama; Masao Fukuda
Journal:  J Bacteriol       Date:  2004-05       Impact factor: 3.490

6.  Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme.

Authors:  X Peng; T Egashira; K Hanashiro; E Masai; S Nishikawa; Y Katayama; K Kimbara; M Fukuda
Journal:  Appl Environ Microbiol       Date:  1998-07       Impact factor: 4.792

7.  Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

Authors:  Yusuke Sato; Hideki Moriuchi; Shojiro Hishiyama; Yuichiro Otsuka; Kenji Oshima; Daisuke Kasai; Masaya Nakamura; Seiji Ohara; Yoshihiro Katayama; Masao Fukuda; Eiji Masai
Journal:  Appl Environ Microbiol       Date:  2009-06-19       Impact factor: 4.792

8.  Cloning and sequencing of the gene for a Pseudomonas paucimobilis enzyme that cleaves beta-aryl ether.

Authors:  E Masai; Y Katayama; S Kawai; S Nishikawa; M Yamasaki; N Morohoshi
Journal:  J Bacteriol       Date:  1991-12       Impact factor: 3.490

9.  How good are my data and what is the resolution?

Authors:  Philip R Evans; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-13

10.  An introduction to data reduction: space-group determination, scaling and intensity statistics.

Authors:  Philip R Evans
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18
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