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Title: Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis

Abstract

Glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis was crystallized and preliminary crystallographic studies of the crystals were performed. Glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis was crystallized and preliminary crystallographic studies of the crystals were performed. Crystals were grown at 293 K by the sitting-drop vapour-diffusion method. Native X-ray diffraction data were collected to 2.4 Å resolution using synchrotron radiation at station BL44XU of SPring-8. The crystal belongs to the rhombohedral space group R3, with unit-cell parameters a = b = 217.48, c = 66.48 Å. Assuming the presence of two molecules in the asymmetric unit, the V{sub M} value was 2.7 Å{sup 3} Da{sup −1} and the solvent content was 54.1%. The protein was also cocrystallized with substrates and diffraction data were collected to 2.7 Å resolution.

Authors:
; ;  [1];  [2];  [3];  [1];  [3];  [1]
  1. Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan)
  2. Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan)
  3. (Sosho Project), JST, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan)
Publication Date:
OSTI Identifier:
22360258
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section F; Journal Volume: 63; Journal Issue: Pt 2; Other Information: PMCID: PMC2330122; PMID: 17277457; PUBLISHER-ID: fw5119; OAI: oai:pubmedcentral.nih.gov:2330122; Copyright (c) International Union of Crystallography 2007; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United Kingdom
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; CRYSTALLIZATION; CRYSTALS; DIFFUSION; GLYCEROL; MOLECULES; PROTEINS; RESOLUTION; SOLVENTS; SPACE GROUPS; SUBSTRATES; SYNCHROTRON RADIATION; X-RAY DIFFRACTION

Citation Formats

Katsumi, Ryota, Koga, Yuichi, You, Dong-Ju, Matsumura, Hiroyoshi, CREST, Takano, Kazufumi, CREST, and Kanaya, Shigenori, E-mail: kanaya@mls.eng.osaka-u.ac.jp. Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis. United Kingdom: N. p., 2007. Web. doi:10.1107/S1744309107001388.
Katsumi, Ryota, Koga, Yuichi, You, Dong-Ju, Matsumura, Hiroyoshi, CREST, Takano, Kazufumi, CREST, & Kanaya, Shigenori, E-mail: kanaya@mls.eng.osaka-u.ac.jp. Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis. United Kingdom. doi:10.1107/S1744309107001388.
Katsumi, Ryota, Koga, Yuichi, You, Dong-Ju, Matsumura, Hiroyoshi, CREST, Takano, Kazufumi, CREST, and Kanaya, Shigenori, E-mail: kanaya@mls.eng.osaka-u.ac.jp. Thu . "Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis". United Kingdom. doi:10.1107/S1744309107001388.
@article{osti_22360258,
title = {Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis},
author = {Katsumi, Ryota and Koga, Yuichi and You, Dong-Ju and Matsumura, Hiroyoshi and CREST and Takano, Kazufumi and CREST and Kanaya, Shigenori, E-mail: kanaya@mls.eng.osaka-u.ac.jp},
abstractNote = {Glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis was crystallized and preliminary crystallographic studies of the crystals were performed. Glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis was crystallized and preliminary crystallographic studies of the crystals were performed. Crystals were grown at 293 K by the sitting-drop vapour-diffusion method. Native X-ray diffraction data were collected to 2.4 Å resolution using synchrotron radiation at station BL44XU of SPring-8. The crystal belongs to the rhombohedral space group R3, with unit-cell parameters a = b = 217.48, c = 66.48 Å. Assuming the presence of two molecules in the asymmetric unit, the V{sub M} value was 2.7 Å{sup 3} Da{sup −1} and the solvent content was 54.1%. The protein was also cocrystallized with substrates and diffraction data were collected to 2.7 Å resolution.},
doi = {10.1107/S1744309107001388},
journal = {Acta Crystallographica. Section F},
number = Pt 2,
volume = 63,
place = {United Kingdom},
year = {Thu Feb 01 00:00:00 EST 2007},
month = {Thu Feb 01 00:00:00 EST 2007}
}
  • Crystallization of and preliminary crystallographic studies on an active-site mutant of pro-Tk-subtilisin from the hyperthermophilic archaeon T. kodakaraensis were performed. Crystallization of and preliminary crystallographic studies on an active-site mutant of pro-Tk-subtilisin from the hyperthermophilic archaeon Thermococcus kodakaraensis were performed. The crystal was grown at 277 K by the sitting-drop vapour-diffusion method. Native X-ray diffraction data were collected to 2.3 Å resolution using synchrotron radiation from station BL41XU at SPring-8. The crystal belongs to the orthorhombic space group I222, with unit-cell parameters a = 92.69, b = 121.78, c = 77.53 Å. Assuming the presence of one molecule per asymmetricmore » unit, the Matthews coefficient V{sub M} was calculated to be 2.6 Å{sup 3} Da{sup −1} and the solvent content was 53.1%.« less
  • The hyperthermostable thioredoxin peroxidase from the aerobic hyperthermophilic archaeon A. pernix K1 was crystallized. The crystal diffracted to 2.7 Å resolution.
  • Ferritin from P. furiosus crystallizes in space group C222{sub 1}, with unit-cell parameters a = 258.1, b = 340.1, c = 266.5 Å and 36 monomers in the asymmetric unit, corresponding to one and a half 24-mers. Crystals of the title protein have been produced and preliminary structural analysis has been carried out. The crystals belong to the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 258.1, b = 340.1, c = 266.5 Å. The protein forms a 24-mer of 20 kDa subunits, which assemble with 432 non-crystallographic symmetry. A total of 36 monomers are found in themore » asymmetric unit, corresponding to one and a half 24-mers.« less
  • l-Threonine dehydrogenase from the hyperthermophilic archaeon P. horikoshii was crystallized and preliminary X-ray crystallographic analysis was carried out. Recombinant l-threonine dehydrogenase from the hyperthermophilic archaeon Pyrococcus horikoshii was prepared using an Escherichia coli expression system. The hyperthermostable l-threonine dehydrogenase consists of 348 amino acids with a molecular weight of 37.7 kDa. The enzyme was crystallized by the hanging-drop vapour-diffusion method at 277 K and preliminary X-ray crystallographic analysis was carried out. Diffraction data were collected to 2.20 Å resolution under cryogenic conditions. P. horikoshiil-threonine dehydrogenase crystals belong to space group I4{sub 1}22, with unit-cell parameters a = b = 143.84,more » c = 304.13 Å. The presence of three subunits of the enzyme per asymmetric unit was estimsted to give a Matthews coefficient (V{sub M}) of 3.5 Å{sup 3} Da{sup −1} and a solvent content of 64.7%(v/v)« less
  • A putative ribosomal RNA-processing factor consisting of two KH domains from Pyrococcus horikoshii OT3 (PH1566; 25 kDa) was crystallized by the sitting-drop vapour-diffusion method using PEG 3000 as the precipitant. The space group of the crystals was determined as primitive orthorhombic P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 45.9, b = 47.4, c = 95.7 Å. A putative ribosomal RNA-processing factor consisting of two KH domains from Pyrococcus horikoshii OT3 (PH1566; 25 kDa) was crystallized by the sitting-drop vapour-diffusion method using PEG 3000 as the precipitant. The crystals diffracted X-rays to beyond 2.0 Å resolution using a synchrotron-radiationmore » source. The space group of the crystals was determined as primitive orthorhombic P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 45.9, b = 47.4, c = 95.7 Å. The crystals contain one molecule in the asymmetric unit (V{sub M} = 2.5 Å{sup 3} Da{sup −1}) and have a solvent content of 50%.« less