scholarly journals Overproduction, crystallization and preliminary X-ray crystallographic analysis ofEscherichia colitRNAN6-threonylcarbamoyladenosine dehydratase

2014 ◽  
Vol 70 (11) ◽  
pp. 1517-1520 ◽  
Author(s):  
Sunmin Kim ◽  
Keon Young Kim ◽  
Jeong Kuk Park ◽  
Byung Il Lee ◽  
Yun-Gon Kim ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
X Rays ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
E Coli ◽  
Protein Mass ◽  
Crystal Volume

Escherichia colitRNAN6-threonylcarbamoyladenosine dehydratase (TcdA), previously called CsdL or YgdL, was overproduced and purified fromE. coliand crystallized using polyethylene glycol 3350 as a crystallizing agent. X-ray diffraction data were collected to 2.70 Å resolution under cryoconditions using synchrotron X-rays. The crystals belonged to space groupP21, with unit-cell parametersa= 65.4,b= 96.8,c= 83.3 Å, β = 111.7°. According to the Matthews coefficient, the asymmetric unit may contain up to four subunits of the monomeric protein, with a crystal volume per protein mass (VM) of 2.12 Å3 Da−1and 42.1% solvent content.

Preliminary X-ray crystallographic analysis of Bowman–Birk trypsin inhibitor from barley seeds

1998 ◽  
Vol 54 (3) ◽  
pp. 441-443 ◽  
Author(s):  
Hyun Kyu Song ◽  
Se Won Suh
Keyword(s):  
Trypsin Inhibitor ◽  
Room Temperature ◽  
Crystallographic Analysis ◽  
X Rays ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Protein Mass ◽  
Crystal Volume

Bowman–Birk trypsin inhibitor from barley seeds has been crystallized at room temperature using polyethylene glycol as precipitant. The crystal is tetragonal, belonging to the space group P41212 (or P43212), with unit cell parameters of a = b = 62.48 and c = 94.63 Å. The asymmetric unit contains one molecule of Bowman–Birk trypsin inhibitor with corresponding crystal volume per protein mass (Vm ) of 2.89 Å3 Da−1 and the solvent content of 57% by volume. The crystals diffract to at least 1.9 Å Bragg spacing upon exposure to synchrotron X-rays. X-ray data to 1.9 Å have been collected from a native crystal.

Lactate dehydrogenase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray analysis

2000 ◽  
Vol 56 (1) ◽  
pp. 81-83 ◽  
Author(s):  
Byung Il Lee ◽  
Changsoo Chang ◽  
Seung-Je Cho ◽  
Gye Won Han ◽  
Yeon Gyu Yu ◽  
...  
Keyword(s):  
Type I ◽  
X Rays ◽  
Type Ii ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Protein Mass ◽  
Crystal Volume

L(+)-Lactate dehydrogenase (LDH) is a key enzyme in anaerobic metabolism which converts pyruvate to lactate. LDH from the hyperthermophilic archaebacterium Methanococcus jannaschii has been overexpressed in Escherichia coli and crystallized in two crystal forms at 297 K using 2-methyl-2,4-pentanediol as precipitant. Type I crystals grew rapidly and diffracted to at least 2.8 Å Bragg spacing upon exposure to Cu Kα X-rays. X-ray diffraction data to 2.9 Å have been collected from a native crystal. The type I crystal is tetragonal, belonging to the space group P42212, with unit-cell parameters a = b = 99.74, c = 170.00 Å. The asymmetric unit contains two LDH subunits, with a corresponding crystal volume per protein mass (V m ) of 3.05 Å3 Da−1 and a solvent content of 59.7%. Type II crystals, which grew more slowly, diffracted to at least 1.8 Å Bragg spacing upon exposure to Cu Kα X-rays. X-ray diffraction data to 1.9 Å have been collected from a native crystal. The type II crystal is orthorhombic, belonging to the space group P21212, with unit-cell parameters a = 47.65, b = 125.10, c = 58.08 Å. The asymmetric unit contains a single LDH subunit, with a corresponding crystal volume per protein mass (V m ) of 2.50 Å3 Da−1 and a solvent content of 50.8%. Therefore, the type II crystal is more suitable for high-resolution structure determination than the type I crystal.

scholarly journals Crystallization and preliminary X-ray analysis of the C-terminal fragment of Ski7 fromSaccharomyces cerevisiae

2014 ◽  
Vol 70 (9) ◽  
pp. 1252-1255 ◽  
Author(s):  
Ji-Young Lee ◽  
Si Hoon Park ◽  
Byung-Cheon Jeong ◽  
Hyun Kyu Song
Keyword(s):  
Critical Role ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Protein Mass ◽  
Terminal Fragment ◽  
Mad Phasing ◽  
Mrna Surveillance ◽  
Crystal Volume

Ski7 (superkiller protein 7) plays a critical role in the mRNA surveillance pathway. The C-terminal fragment of Ski7 (residues 520–747) fromSaccharomyces cerevisiaewas heterologously expressed inEscherichia coliand purified to homogeneity. It was successfully crystallized and preliminary X-ray data were collected to 2.0 Å resolution using synchrotron radiation. The crystal belonged to a trigonal space group, eitherP3121 orP3221, with unit-cell parametersa=b= 73.5,c= 83.6 Å. The asymmetric unit contains one molecule of the C-terminal fragment of Ski7 with a corresponding crystal volume per protein mass (VM) of 2.61 Å3 Da−1and a solvent content of 52.8% by volume. The mergingRfactor is 6.6%. Structure determination by MAD phasing is under way.

Crystallization and preliminary X-ray diffraction study of lactonohydrolase from Fusarium oxysporum

1998 ◽  
Vol 54 (6) ◽  
pp. 1432-1434 ◽  
Author(s):  
Michihiko Kataoka ◽  
Kazuhiko Yamamoto ◽  
Sakayu Shimizu ◽  
Mayumi Ohta ◽  
Akiko Kita ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Polyethylene Glycol 4000 ◽  
X Ray ◽  
Cell Parameters ◽  
Vapour Diffusion ◽  
Crystal Volume

The lactonohydrolase from the fungus Fusarium oxysporum AKU 3702 was crystallized by the vapour-diffusion procedure in the presence of polyethylene glycol 4000 as a precipitant. The crystals belong to the monoclinic space group P21 with unit-cell parameters a = 156, b = 100, c = 94.1 Å, β = 91.7°. Assuming that there are two lactonohydrolase-dimer molecules in the asymmetric unit, the crystal volume per unit molecular mass, Vm , is calculated to be 2.94 Å3 Da−1.

scholarly journals Expression, purification and preliminary crystallographic analysis ofMycobacterium tuberculosisCysQ, a phosphatase involved in sulfur metabolism

2014 ◽  
Vol 70 (6) ◽  
pp. 750-753 ◽  
Author(s):  
Anna I. Erickson ◽  
Reta D. Sarsam ◽  
Andrew J. Fisher
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Sulfur Metabolism ◽  
Crystallographic Analysis ◽  
Transfer Reactions ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters

CysQ is part of the sulfur-activation pathway that dephosphorylates 3′-phosphoadenosine 5′-monophosphate (PAP) to regenerate adenosine 5′-monophosphate (AMP) and free phosphate. PAP is the product of sulfate-transfer reactions from sulfotransferases that use the universal sulfate donor 3′-phosphoadenosine 5′-phosphosulfate (PAPS). In some organisms PAP is also the product of PAPS reductases that reduce sulfate from PAPS to sulfite. CysQ fromMycobacterium tuberculosis, which plays an important role in the biosynthesis of sulfated glycoconjugates, was successfully purified and crystallized in 24% PEG 1500, 20% glycerol. X-ray diffraction data were collected to 1.7 Å resolution using a synchrotron-radiation source. Crystals grew in the orthorhombic space groupP212121, with unit-cell parametersa= 40.3,b= 57.9,c= 101.7 Å and with one monomer per asymmetric unit.

scholarly journals Crystallographic analysis of RsmA, a ribosomal RNA small subunit methyltransferase A fromStaphylococcus aureus

2015 ◽  
Vol 71 (8) ◽  
pp. 1063-1066 ◽  
Author(s):  
Yang Liu ◽  
Yuwei Zhu ◽  
Maikun Teng ◽  
Xu Li
Keyword(s):  
Staphylococcus Aureus ◽  
Ribosomal Rna ◽  
Small Subunit ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Rotation Function

RsmA, a ribosomal RNA small subunit methyltransferase fromStaphylococcus aureus, catalyzes theN6methylation of adenine in 16S rRNA. In this study, RsmA fromStaphylococcus aureuswas cloned, expressed, purified and crystallized. The crystal belonged to space groupC2, with unit-cell parametersa= 84.38,b= 157.76,c= 96.50 Å, β = 95.04°. X-ray diffraction data were collected to a resolution of 3.2 Å. The self-rotation function and the Matthews coefficient suggested the presence of two molecules in the asymmetric unit.

scholarly journals Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation

2014 ◽  
Vol 70 (9) ◽  
pp. 1236-1239 ◽  
Author(s):  
Kan Kobayashi ◽  
Takehiro Suzuki ◽  
Naoshi Dohmae ◽  
Ryuichiro Ishitani ◽  
Osamu Nureki
Keyword(s):  
Elongation Factor ◽  
Crystallographic Analysis ◽  
X Rays ◽  
Asymmetric Unit ◽  
Post Translational Modification ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Crystallization Method

Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein fromEscherichia coliwas overexpressed, purified and crystallized. The crystal of YfcM was obtained by thein situproteolysis crystallization method and diffracted X-rays to 1.45 Å resolution. It belonged to space groupC2, with unit-cell parametersa= 124.4,b= 37.0,c= 37.6 Å, β = 101.2°. The calculated Matthews coefficient (VM) of the crystal was 1.91 Å3 Da−1, indicating that one YfcM molecule is present in the asymmetric unit with a solvent content of 35.7%.

scholarly journals Crystallization and preliminary X-ray crystallographic analysis of ribosome assembly factors: the Rpf2–Rrs1 complex

2014 ◽  
Vol 70 (12) ◽  
pp. 1649-1652 ◽  
Author(s):  
Nozomi Asano ◽  
Akiyoshi Nakamura ◽  
Keisuke Komoda ◽  
Koji Kato ◽  
Isao Tanaka ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Essential Proteins ◽  
Unit Structure

Rpf2 and Rrs1 are essential proteins for ribosome biogenesis. These proteins form a complex (the Rpf2-subcomplex) with 5S rRNA and two ribosomal proteins (L5 and L11). This complex is recruited to the ribosome precursor (the 90S pre-ribosome). This recruitment is necessary for the maturation of 25S rRNA. Genetic depletion of Rpf2 and Rrs1 results in accumulation of the 25S rRNA precursor. In this study, Rpf2 and Rrs1 fromAspergillus nidulanswere co-overexpressed inEscherichia coli, purified and crystallized. Subsequent analysis revealed that these crystals contained the central core region of the complex consisting of both N-terminal domains. X-ray diffraction data were collected to 2.35 Å resolution. Preliminary analysis revealed that the crystals belonged to space groupP212121, with unit-cell parametersa= 54.1,b= 123.3,c = 133.8 Å. There are two complexes in the asymmetric unit. Structure determination using selenomethionine-labelled protein is in progress.

scholarly journals Ectodomain of plasmodesmata-localized protein 5 inArabidopsis: expression, purification, crystallization and crystallographic analysis

2017 ◽  
Vol 73 (9) ◽  
pp. 532-535 ◽  
Author(s):  
Xiaocui Wang ◽  
Peiyan Zhu ◽  
Shanshan Qu ◽  
Jie Zhao ◽  
Prashant K. Singh ◽  
...  
Keyword(s):  
Expression System ◽  
Cell Movement ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Crystal Content

Plasmodesmata-localized protein 5 (PDLP5) is a cysteine-rich receptor-like protein which is localized on the plasmodesmata ofArabidopsis thaliana. Overexpression of PDLP5 can reduce the permeability of the plasmodesmata and further affect the cell-to-cell movement of viruses and macromolecules in plants. The ectodomain of PDLP5 contains two DUF26 domains; however, the function of these domains is still unknown. Here, the ectodomain of PDLP5 fromArabidopsiswas cloned and overexpressed using an insect expression system and was then purified and crystallized. X-ray diffraction data were collected to 1.90 Å resolution and were indexed in space groupP1, with unit-cell parametersa= 41.9,b= 48.1,c = 62.2 Å, α = 97.3, β = 103.1, γ = 99.7°. Analysis of the crystal content indicated that there are two molecules in the asymmetric unit, with a Matthews coefficient of 2.51 Å3 Da−1and a solvent content of 50.97%.

scholarly journals Crystallization and preliminary X-ray crystallographic analysis of Z-ring-associated protein (ZapD) fromEscherichia coli

2015 ◽  
Vol 71 (2) ◽  
pp. 194-198 ◽  
Author(s):  
Sang Hyeon Son ◽  
Hyung Ho Lee
Keyword(s):  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Polyethylene Glycol 400 ◽  
X Ray ◽  
Cell Parameters ◽  
Protein Mass ◽  
Division Site ◽  
Reservoir Solution ◽  
Z Ring ◽  
Crystal Volume

Bacterial cytokinesis is accomplished by the Z-ring, which is a polymeric structure that includes the tubulin homologue FtsZ at the division site. ZapD, a Z-ring-associated protein, directly binds to FtsZ and stabilizes the polymerization of FtsZ to form a stable Z-ring during cytokinesis. Structural analysis of ZapD fromEscherichia coliwas performed to investigate the mechanism of ZapD-mediated FtsZ stabilization and polymerization. ZapD was crystallized using a reservoir solution consisting of 1.5 Mlithium sulfate, 0.1 MHEPES pH 7.8, 2%(v/v) polyethylene glycol 400. X-ray diffraction data were collected to 2.95 Å resolution. The crystals belonged to the hexagonal space groupP64, with unit-cell parametersa=b= 109.5,c= 106.7 Å, γ = 120.0°. Two monomers were present in the asymmetric unit, resulting in a crystal volume per protein mass (VM) of 3.25 Å3Da−1and a solvent content of 62.17%.

Sign in / Sign up

Export Citation Format

Share Document