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Title: Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe–2S] ferredoxin derived from Pseudomonas sp. strain KKS102

Abstract

The reduced form of BphA3, a Rieske-type [2Fe–2S] ferredoxin, was crystallized by the sitting-drop vapour-diffusion method under anaerobic conditions. A molecular-replacement calculation yielded a satisfactory solution. The reduced form of BphA3, a Rieske-type [2Fe–2S] ferredoxin component of the biphenyl dioxygenase BphA from Pseudomonas sp. strain KKS102, was crystallized by the sitting-drop vapour-diffusion method under anaerobic conditions. The crystal belongs to space group P3{sub 1}21, with unit-cell parameters a = b = 49.6, c = 171.9 Å, and diffracts to a resolution of 1.95 Å. A molecular-replacement calculation using oxidized BphA3 as a search model yielded a satisfactory solution.

Authors:
 [1];  [2];  [3];  [4];  [5]
  1. Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064 (Japan)
  2. Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Hyogo 678-1297 (Japan)
  3. Department of Biomolecular Functional Engineering, University of Ibaraki, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511 (Japan)
  4. Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064 (Japan)
  5. (JBIRC), Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064 (Japan)
Publication Date:
OSTI Identifier:
22360307
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section F; Journal Volume: 63; Journal Issue: Pt 4; Other Information: PMCID: PMC2330217; PMID: 17401203; PUBLISHER-ID: ll5102; OAI: oai:pubmedcentral.nih.gov:2330217; 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; BIPHENYL; CRYSTALLIZATION; CRYSTALS; DIFFUSION; ELECTRON TRANSFER; MATHEMATICAL SOLUTIONS; OXYGEN; RESOLUTION; SOLUTIONS; SPACE GROUPS; STRAINS

Citation Formats

Senda, Miki, Kishigami, Shinya, Kimura, Shigenobu, Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp, and Japan Biological Information Research Center. Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe–2S] ferredoxin derived from Pseudomonas sp. strain KKS102. United Kingdom: N. p., 2007. Web. doi:10.1107/S1744309107009992.
Senda, Miki, Kishigami, Shinya, Kimura, Shigenobu, Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp, & Japan Biological Information Research Center. Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe–2S] ferredoxin derived from Pseudomonas sp. strain KKS102. United Kingdom. doi:10.1107/S1744309107009992.
Senda, Miki, Kishigami, Shinya, Kimura, Shigenobu, Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp, and Japan Biological Information Research Center. Sun . "Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe–2S] ferredoxin derived from Pseudomonas sp. strain KKS102". United Kingdom. doi:10.1107/S1744309107009992.
@article{osti_22360307,
title = {Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe–2S] ferredoxin derived from Pseudomonas sp. strain KKS102},
author = {Senda, Miki and Kishigami, Shinya and Kimura, Shigenobu and Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp and Japan Biological Information Research Center},
abstractNote = {The reduced form of BphA3, a Rieske-type [2Fe–2S] ferredoxin, was crystallized by the sitting-drop vapour-diffusion method under anaerobic conditions. A molecular-replacement calculation yielded a satisfactory solution. The reduced form of BphA3, a Rieske-type [2Fe–2S] ferredoxin component of the biphenyl dioxygenase BphA from Pseudomonas sp. strain KKS102, was crystallized by the sitting-drop vapour-diffusion method under anaerobic conditions. The crystal belongs to space group P3{sub 1}21, with unit-cell parameters a = b = 49.6, c = 171.9 Å, and diffracts to a resolution of 1.95 Å. A molecular-replacement calculation using oxidized BphA3 as a search model yielded a satisfactory solution.},
doi = {10.1107/S1744309107009992},
journal = {Acta Crystallographica. Section F},
number = Pt 4,
volume = 63,
place = {United Kingdom},
year = {Sun Apr 01 00:00:00 EDT 2007},
month = {Sun Apr 01 00:00:00 EDT 2007}
}
  • The electron-transfer complex of BphA3, a Rieske-type [2Fe–2S] ferredoxin, and BphA4, a NADH-dependent ferredoxin reductase, was crystallized by the sitting-drop vapour-diffusion method under anaerobic conditions. The electron-transfer complex of BphA3, a Rieske-type [2Fe–2S] ferredoxin, and BphA4, a NADH-dependent ferredoxin reductase, was crystallized using the sitting-drop vapour-diffusion method under anaerobic conditions. The obtained crystals were analyzed by SDS–PAGE, which showed that they contained both BphA3 and BphA4. The crystals belong to space group P2{sub 1}, with unit-cell parameters a = 60.60, b = 173.72, c = 60.98 Å, β = 115.8°, and diffracted to a resolution of 1.9 Å.
  • BphA3, a Rieske-type [2Fe–2S] ferredoxin, was crystallized by the hanging-drop vapour-diffusion method. A molecular-replacement calculation yielded a satisfactory solution. BphA3, a Rieske-type [2Fe–2S] ferredoxin component of a biphenyl dioxygenase (BphA) from Pseudomonas sp. strain KKS102, was crystallized by the hanging-drop vapour-diffusion method. Two crystal forms were obtained from the same conditions. The form I crystal belongs to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 26.3, b = 144.3, c = 61.5 Å, and diffracted to 2.45 Å resolution. The form II crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 26.2, bmore » = 121.3, c = 142.7 Å, and diffracted to 2.8 Å resolution. A molecular-replacement calculation using BphF as a search model yielded a satisfactory solution for both forms.« less
  • A vertebrate-type [2Fe–2S] ferredoxin (FdxB), which is probably involved in the iron–sulfur cluster-biosynthesis system of the γ-proteobacterium P. putida JCM 20004, has been crystallized in space group P6{sub 1}22. The needle-shaped crystals of recombinant FdxB diffract to 1.90 Å resolution using synchrotron radiation. The iron–sulfur (Fe–S) cluster-biosynthesis (ISC) system of the γ-proteobacterium Pseudomonas putida JCM 20004 contains a constitutively expressed vertebrate-type [2Fe–2S] ferredoxin, FdxB, which lacks the conserved free cysteine residue near the Fe–S cluster site that has been proposed to function in the catalysis of biological Fe–S cluster assembly in other bacterial homologues. Recombinant FdxB was heterologously overproduced inmore » Escherichia coli, purified and crystallized in its oxidized form by the hanging-drop vapour-diffusion and streak-seeding methods using 1.6 M trisodium citrate dihydrate pH 6.5. The thin needle-shaped crystals diffract to 1.90 Å resolution and belong to the hexagonal space group P6{sub 1}22, with unit-cell parameters a = 87.58, c = 73.14 Å. The asymmetric unit contains one protein molecule.« less
  • The amidase domain of the allophanate hydrolase AtzF from Pseudomonas sp. strain ADP has been crystallized and preliminary X-ray diffraction data have been collected. The allophanate hydrolase from Pseudomonas sp. strain ADP was expressed and purified, and a tryptic digest fragment was subsequently identified, expressed and purified. This 50 kDa construct retained amidase activity and was crystallized. The crystals diffracted to 2.5 Å resolution and adopted space group P2{sub 1}, with unit-cell parameters a = 82.4, b = 179.2, c = 112.6 Å, β = 106.6°.
  • The electron-transfer complex between the terminal oxygenase and ferredoxin of carbazole 1,9a-dioxygenase was crystallized and diffraction data were collected to 1.90 Å resolution. Carbazole 1,9a-dioxygenase, which consists of an oxygenase component (CARDO-O) and the electron-transport components ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R), catalyzes dihydroxylation at the C1 and C9a positions of carbazole. The electron-transport complex between CARDO-O and CARDO-F crystallizes at 293 K using hanging-drop vapour diffusion with the precipitant PEG MME 2000 (type I crystals) or PEG 3350 (type II). Blossom-shaped crystals form from a pile of triangular plate-shaped crystals. The type I crystal diffracts to a maximum resolutionmore » of 1.90 Å and belongs to space group P2{sub 1}, with unit-cell parameters a = 97.1, b = 89.8, c = 104.9 Å, α = γ = 90, β = 103.8°. Diffraction data for the type I crystal gave an overall R{sub merge} of 8.0% and a completeness of 100%. Its V{sub M} value is 2.63 Å{sup 3} Da{sup −1}, indicating a solvent content of 53.2%.« less