scholarly journals Crystallographic analysis of NosA, which catalyzes terminal amide formation in the biosynthesis of nosiheptide

2015 ◽  
Vol 71 (8) ◽  
pp. 1033-1037 ◽  
Author(s):  
Yanting Wang ◽  
Shanshan Liu ◽  
Pengfei Yao ◽  
Yi Yu ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Diffraction Data ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Cell Parameters ◽  
Vapour Diffusion ◽  
Streptomyces Actuosus

Nosiheptide is a member of the thiopeptide family of antibiotics which demonstrates potent activities against various bacterial pathogens. The formation of its C-terminal amide is catalysed by NosA in an unusual strategy for maturating certain thiopeptides by processing precursor peptides featuring a serine extension. Here, a recombinant C-terminally truncated selenomethionine-derivatized NosA1–111variant fromStreptomyces actuosusconsisting of residues 1–111, named SeMet NosA1–111, was crystallized using the sitting-drop vapour-diffusion method. Diffraction data were collected to 2.40 Å resolution using synchrotron radiation. The crystals belonged to the primitive cubic space groupP4132, with unit-cell parametersa=b=c= 143.3 Å. Assuming the presence of three molecules in the asymmetric unit, the calculated Matthews coefficient was 3.94 Å3 Da−1and the corresponding solvent content was 40.3%.

scholarly journals Crystallization and preliminary X-ray crystallographic analysis of human myotubularin-related protein 1

2015 ◽  
Vol 71 (3) ◽  
pp. 261-265 ◽  
Author(s):  
Seoung Min Bong ◽  
Seung Won Yang ◽  
Ji-Woong Choi ◽  
Seung Jun Kim ◽  
Byung Il Lee
Keyword(s):  
Escherichia Coli ◽  
Polyethylene Glycol ◽  
Synchrotron Radiation ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
Related Protein ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters

Myotubularin-related protein 1 is a phosphatase that dephosphorylates phospholipids such as phosphatidylinositol 3-phosphate or phosphatidylinositol 3,5-bisphosphate. In this study, human MTMR1 was overexpressed inEscherichia coli, purified and crystallized at 277 K using polyethylene glycol 20 000 as a precipitant. Diffraction data were collected to 2.0 Å resolution using synchrotron radiation. The crystals belonged to space groupP1, with unit-cell parametersa= 67.219,b= 96.587,c= 97.581 Å, α = 87.597, β = 86.072, γ = 77.327°. Assuming the presence of four molecules in the asymmetric unit, the calculated Matthews coefficient value was 2.61 Å3 Da−1and the corresponding solvent content was 52.9%.

scholarly journals Cloning, purification and preliminary X-ray crystallographic analysis of the OmpA-like domain of peptidoglycan-associated lipoprotein fromAcinetobacter baumannii

2012 ◽  
Vol 68 (11) ◽  
pp. 1351-1353 ◽  
Author(s):  
Jung Hyun Song ◽  
Woo Cheol Lee ◽  
Jeong Soon Park ◽  
Seung Il Kim ◽  
Je Chul Lee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Acinetobacter Baumannii ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Vapour Diffusion ◽  
Strain Bl21

Peptidoglycan-associated lipoprotein (Pal) is one component of the Tol–Pal system that is involved in maintaining the integrity and stability of the outer membrane. The C-terminal OmpA-like domain of Pal interacts noncovalently with peptidoglycan. In this study, the OmpA-like domain of Pal fromAcinetobacter baumanniiwas overexpressed inEscherichia colistrain BL21 (DE3), purified and crystallized using the vapour-diffusion method. A native crystal diffracted to 1.4 Å resolution and belonged to space groupP61orP65, with unit-cell parametersa=b= 72.58,c= 44.65 Å, a calculated Matthews coefficient of 2.64 Å3 Da−1and one molecule per asymmetric unit.

scholarly journals Crystallization and preliminary X-ray analysis of the NAD+-reducing [NiFe] hydrogenase fromHydrogenophilus thermoluteolusTH-1

2015 ◽  
Vol 71 (1) ◽  
pp. 96-99 ◽  
Author(s):  
Midori Taketa ◽  
Hanae Nakagawa ◽  
Mao Habukawa ◽  
Hisao Osuka ◽  
Kiyohito Kihira ◽  
...  
Keyword(s):  
Diffusion Method ◽  
Asymmetric Unit ◽  
Dispersion Method ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Vapour Diffusion ◽  
Anomalous Signal ◽  
Th 1

NAD+-reducing [NiFe] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of NAD+and NADH. Here, the isolation, purification and crystallization of the NAD+-reducing [NiFe] hydrogenase fromHydrogenophilus thermoluteolusTH-1 are reported. Crystals of the NAD+-reducing [NiFe] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. The crystal diffracted to 2.58 Å resolution and belonged to space groupC2, with unit-cell parametersa= 131.43,b= 189.71,c= 124.59 Å, β = 109.42°. Assuming the presence of two NAD+-reducing [NiFe] hydrogenase molecules in the asymmetric unit,VMwas calculated to be 2.2 Å3 Da−1, which corresponds to a solvent content of 43%. Initial phases were determined by the single-wavelength anomalous dispersion method using the anomalous signal from the Fe atoms.

scholarly journals Crystallization and crystallographic analysis of branching enzymes fromCyanothecesp. ATCC 51142

2015 ◽  
Vol 71 (8) ◽  
pp. 1109-1113 ◽  
Author(s):  
Mari Hayashi ◽  
Ryuichiro Suzuki ◽  
Christophe Colleoni ◽  
Steven G. Ball ◽  
Naoko Fujita ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Cyanobacterial Species ◽  
Vapour Diffusion ◽  
Branching Enzymes

Several cyanobacterial species, includingCyanothecesp. ATCC 51142, remarkably have four isoforms of α-glucan branching enzymes (BEs). Based on their primary structures, they are classified into glycoside hydrolase (GH) family 13 (BE1, BE2 and BE3) or family 57 (GH57 BE). In the present study, GH13-type BEs fromCyanothecesp. ATCC 51142 (BE1, BE2 and BE3) have been overexpressed inEscherichia coliand biochemically characterized. The recombinant BE1 was crystallized by the hanging-drop vapour-diffusion method. Crystals of BE1 were obtained at 293 K in the presence of 0.2 MMg2+, 7–10%(w/v) ethanol, 0.1 MHEPES–NaOH pH 7.2–7.9. The crystals belonged to the tetragonal space groupP41212, with unit-cell parametersa = b = 133.75,c= 185.90 Å, and diffracted to beyond 1.85 Å resolution. Matthews coefficient calculations suggested that the crystals of BE1 contained two molecules in the asymmetric unit.

scholarly journals Crystallization and X-ray analysis ofD-threonine aldolase fromChlamydomonas reinhardtii

2017 ◽  
Vol 73 (2) ◽  
pp. 86-89
Author(s):  
Yuki Hirato ◽  
Masaru Goto ◽  
Mayumi Tokuhisa ◽  
Minoru Tanigawa ◽  
Katsushi Nishimura
Keyword(s):  
Diffusion Method ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Threonine Aldolase ◽  
Vapour Diffusion ◽  
Resolution Analysis

D-Threonine aldolase from the green algaChlamydomonas reinhardtii(CrDTA) catalyzes the interconversion of several β-hydroxy-D-amino acids (e.g.D-threonine) and glycine plus the corresponding aldehydes. Recombinant CrDTA was overexpressed inEscherichia coliand purified to homogeneity; it was subsequently crystallized using the hanging-drop vapour-diffusion method at 295 K. Data were collected and processed at 1.85 Å resolution. Analysis of the diffraction pattern showed that the crystal belonged to space groupP1, with unit-cell parametersa= 64.79,b= 74.10,c= 89.94 Å, α = 77.07, β = 69.34, γ = 71.93°. The asymmetric unit contained four molecules of CrDTA. The Matthews coefficient was calculated to be 2.12 Å3 Da−1and the solvent content was 41.9%.

scholarly journals Crystallographic analysis of FAD-dependent glucose dehydrogenase

2015 ◽  
Vol 71 (8) ◽  
pp. 1017-1019 ◽  
Author(s):  
Hirofumi Komori ◽  
Koji Inaka ◽  
Naoki Furubayashi ◽  
Michinari Honda ◽  
Yoshiki Higuchi
Keyword(s):  
Aspergillus Terreus ◽  
Glucose Dehydrogenase ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Data Set ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters

An FAD-dependent glucose dehydrogenase (GDH) fromAspergillus terreuswas purified and crystallized at 293 K using the sitting-drop vapour-diffusion method. A data set was collected to a resolution of 1.6 Å from a single crystal at 100 K using a rotating-anode X-ray source. The crystal belonged to space groupP21, with unit-cell parametersa= 56.56,b= 135.74,c= 74.13 Å, β = 90.37°. The asymmetric unit contained two molecules of GDH. The Matthews coefficient was calculated to be 2.2 Å3 Da−1and the solvent content was estimated to be 44%.

Crystallization and preliminary X-ray crystallographic analysis of a vancomycin–N-acetyl-D-Ala-D-Ala complex

1999 ◽  
Vol 55 (2) ◽  
pp. 534-535 ◽  
Author(s):  
Deborah McPhail ◽  
Alan Cooper ◽  
Andy Freer
Keyword(s):  
Room Temperature ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
The Novel ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Crystal Density

A vancomycin–N-acetyl-D-Ala-D-Ala complex has been crystallized by the sitting-drop vapour-diffusion method using imidazole maleic buffer at pH 7.6. The novel crystals obtained belong to the space group P6322 with unit-cell parameters a = b = 73.43 (1), c = 277.17 (4) Å, γ = 120°. The crystal density was determined as 1.106 g cm−3 which gives a supercell of 24 molecules (12 dimers) per asymmetric unit for an acceptable Matthews number and an estimated solvent content of 42%. Data were collected at room temperature to 2.8 Å.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

scholarly journals Crystallographic analysis of the Staphylococcus epidermidis lipase involved in esterification in aqueous solution

2018 ◽  
Vol 74 (6) ◽  
pp. 351-354
Author(s):  
Cheng-Huan Liu ◽  
Yu-Ting Chen ◽  
Ming-Hon Hou ◽  
Nien-Jen Hu ◽  
Chin-Shuh Chen ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Molecular Weight ◽  
Staphylococcus Epidermidis ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Data Set ◽  
Solvent Content ◽  
Cell Parameters ◽  
Esterification In Aqueous Solution

The Staphylococcus epidermidis lipase (SeLip, GehC) can be used in flavour-compound production via esterification in aqueous solution. This study reports the crystallization and crystallographic analysis of recombinant GehC (rGehC; Lys303–Lys688) with a molecular weight of 43 kDa. rGehC was crystallized at 293 K using PEG 10 000 as a precipitant, and a 99.9% complete native data set was collected from a cooled crystal at 77 K to a resolution of 1.9 Å with an overall R merge value of 7.3%. The crystals were orthorhombic and belonged to space group P212121, with unit-cell parameters a = 42.07, b = 59.31, c = 171.30 Å, α = β = γ = 90°. Solvent-content calculations suggest that there is likely to be one lipase subunit in the asymmetric unit.

scholarly journals Purification, crystallization and preliminary X-ray crystallographic analysis of the UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF) fromAcinetobacter baumannii

2014 ◽  
Vol 70 (7) ◽  
pp. 976-978 ◽  
Author(s):  
Young Jun An ◽  
Chang-Sook Jeong ◽  
Jeong Hee Yu ◽  
Kyung Min Chung ◽  
Sun-Shin Cha
Keyword(s):  
Multidrug Resistant ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Peptidoglycan Biosynthesis ◽  
Crystallization Method ◽  
Global Spread

The emergence and global spread of multidrug-resistantAcinetobacter baumanniistrains are major threats to public health. Inhibition of peptidoglycan biosynthesis is an effective strategy for the development of antibiotics. The ATP-dependent UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF) that is responsible for the last step of peptidoglycan biosynthesis is a validated target for the development of antibiotics. Crystals ofA. baumanniiMurF in complex with ATP were grown by the microbatch crystallization method at 295 K. The crystals belonged to space groupP3221, with unit-cell parametersa=b= 85.42,c= 129.86 Å. Assuming the presence of one molecule in the asymmetric unit, the solvent content was estimated to be about 54.32%.

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