scholarly journals Crystallization and preliminary X-ray crystallographic analysis of the sclerostin-neutralizing Fab AbD09097

2015 ◽  
Vol 71 (4) ◽  
pp. 388-392 ◽  
Author(s):  
Verena Boschert ◽  
Eva-Maria Muth ◽  
Achim Knappik ◽  
Christian Frisch ◽  
Thomas D. Mueller
Keyword(s):  
Bone Growth ◽  
Antibody Fragment ◽  
Crystallographic Analysis ◽  
Negative Regulator ◽  
X Rays ◽  
X Ray ◽  
Cell Parameters ◽  
Van Buchem Disease ◽  
Cystine Knot Protein ◽  
Canonical Wnt

The secreted cystine-knot protein sclerostin was first identified from genetic screening of patients suffering from the rare bone-overgrowth diseases sclerosteosis and van Buchem disease. Sclerostin acts a negative regulator of bone growth through inhibiting the canonical Wnt signalling cascade by binding to and blocking the Wnt co-receptor LRP5/6. Its function in blocking osteoblastogenesis makes it an important target for osteoanabolic therapy approaches to treat osteoporosis, which is characterized by a progressive decrease in bone mass and density. In this work, the production, crystallization and preliminary X-ray diffraction data analysis of a sclerostin-neutralizing human Fab antibody fragment, AbD09097, obtained from a naive antibody library are reported. Crystals of the Fab AbD09097 belonged to space groupP21, with unit-cell parametersa= 45.19,b= 78.49,c= 59.20 Å, β = 95.71° and diffracted X-rays to a resolution of 1.8 Å.

scholarly journals Crystallization and preliminary X-ray crystallographic analysis of carboxyl-terminal region 4 of SigR fromStreptomyces coelicolorA3(2)

2014 ◽  
Vol 70 (6) ◽  
pp. 747-749
Author(s):  
Keon Young Kim ◽  
Sunmin Kim ◽  
Jeong Kuk Park ◽  
HyoJin Song ◽  
SangYoun Park
Keyword(s):  
Streptomyces Coelicolor ◽  
Crystallographic Analysis ◽  
Terminal Region ◽  
Full Length ◽  
Spectrometric Analysis ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Carboxyl Terminal

Full-length SigR fromStreptomyces coelicolorA3(2) was overexpressed inEscherichia coli, purified and submitted to crystallization trials using either polyethylene glycol 3350 or 4000 as a precipitant. X-ray diffraction data were collected to 2.60 Å resolution under cryoconditions using synchrotron X-rays. The crystal packs in space groupP43212, with unit-cell parametersa=b= 42.14,c= 102.02 Å. According to the Matthews coefficient, the crystal asymmetric unit cannot contain the full-length protein. Molecular replacement with the known structures of region 2 and region 4 as independent search models indicates that the crystal contains only the −35 element-binding carboxyl-terminal region 4 of full-length SigR. Mass-spectrometric analysis of the harvested crystal confirms this, suggesting a crystal volume per protein weight (VM) of 2.24 Å3 Da−1and 45.1% solvent content.

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.

scholarly journals Crystallization and X-ray crystallographic analysis of recombinant TylP, a putative γ-butyrolactone receptor protein fromStreptomyces fradiae

2017 ◽  
Vol 73 (2) ◽  
pp. 109-115 ◽  
Author(s):  
Nurhikmah Mohd-Sharif ◽  
Sofiyah Shaibullah ◽  
Vasanthakumar Givajothi ◽  
Cheng-Seng Tan ◽  
Kok Lian Ho ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
Regulatory Proteins ◽  
Receptor Protein ◽  
X Rays ◽  
Streptomyces Fradiae ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Receptor Proteins ◽  
Cell Parameters ◽  
Reservoir Solution

TylP is one of five regulatory proteins involved in the regulation of antibiotic (tylosin) production, morphological and physiological differentiation inStreptomyces fradiae. Its function is similar to those of various γ-butyrolactone receptor proteins. In this report, N-terminally His-tagged recombinant TylP protein (rTylP) was overproduced inEscherichia coliand purified to homogeneity. The rTylP protein was crystallized from a reservoir solution comprising 34%(v/v) ethylene glycol and 5%(v/v) glycerol. The protein crystals diffracted X-rays to 3.05 Å resolution and belonged to the trigonal space groupP3121, with unit-cell parametersa=b= 126.62,c= 95.63 Å.

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%.

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.

scholarly journals A putative siderophore-interacting protein from the marine bacteriumShewanella frigidimarinaNCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

2016 ◽  
Vol 72 (9) ◽  
pp. 667-671 ◽  
Author(s):  
Inês B. Trindade ◽  
Bruno M. Fonseca ◽  
Pedro M. Matias ◽  
Ricardo O. Louro ◽  
Elin Moe
Keyword(s):  
Iron Acquisition ◽  
Crystallographic Analysis ◽  
Monoclinic Space Group ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Interacting Protein ◽  
X Ray ◽  
Cell Parameters ◽  
Unit Structure ◽  
Shewanella Frigidimarina

Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacteriumShewanella frigidimarinaNCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space groupP21, with unit-cell parametersa= 48.04,b= 78.31,c= 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.

scholarly journals Crystallization and preliminary crystallographic analysis of manganese lipoxygenase

2014 ◽  
Vol 70 (4) ◽  
pp. 522-525 ◽  
Author(s):  
Anneli Wennman ◽  
Ernst H. Oliw ◽  
Saeid Karkehabadi
Keyword(s):  
Expression System ◽  
Crystallographic Analysis ◽  
Gaeumannomyces Graminis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Apparent Homogeneity ◽  
Structural Differences ◽  
Position Specificity ◽  
Take All

Lipoxygenases constitute a family of nonhaem metal enzymes with catalytic iron or, occasionally, catalytic manganese. Lipoxygenases oxidize polyunsaturated fatty acids with position specificity and stereospecificity to hydroperoxides, which contribute to inflammation and the development of cancer. Little is known about the structural differences between lipoxygenases with Fe or Mn and the metal-selection mechanism. APichia pastorisexpression system was used for the production of the manganese lipoxygenase of the take-all fungus of wheat,Gaeumannomyces graminis. The active enzyme was treated with α-mannosidase, purified to apparent homogeneity and subjected to crystal screening and X-ray diffraction. The crystals diffracted to 2.6 Å resolution and belonged to space groupC2, with unit-cell parametersa= 226.6,b= 50.6,c= 177.92 Å, β = 91.70°.

scholarly journals Purification, crystallization and preliminary crystallographic analysis of a 4-thiouridine synthetase–RNA complex

2013 ◽  
Vol 69 (4) ◽  
pp. 421-424 ◽  
Author(s):  
Peter-Thomas Naumann ◽  
Charles T. Lauhon ◽  
Ralf Ficner
Keyword(s):  
Diffraction Data ◽  
Thermotoga Maritima ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Dependent Modification ◽  
Rna Complex

The sulfurtransferase 4-thiouridine synthetase (ThiI) is involved in the ATP-dependent modification of U8 in tRNA. ThiI fromThermotoga maritimawas cloned, overexpressed and purified. A complex comprising ThiI and a truncated tRNA was prepared and crystallized, and X-ray diffraction data were collected to a resolution of 3.5 Å. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 102.9,b= 112.8,c= 132.8 Å.

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 Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp6

2014 ◽  
Vol 70 (6) ◽  
pp. 794-799 ◽  
Author(s):  
Junko Morita ◽  
Kazuki Kato ◽  
Emiko Mihara ◽  
Ryuichiro Ishitani ◽  
Junichi Takagi ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Choline Metabolism ◽  
Protein Molecules ◽  
Membrane Bound

Enpp (ectonucleotide phosphodiesterase/pyrophosphatase) 6 is a membrane-bound glycoprotein that hydrolyzes choline-containing compounds such as lysophosphatidylcholine and glycerophosphorylcholine, and presumably participates in choline metabolism. The catalytic domain of mouse Enpp6 was expressed in HEK293T cells, purified using the TARGET tag/P20.1-Sepharose system and crystallized. An X-ray diffraction data set was collected to 1.8 Å resolution. The crystal belonged to space groupP1, with unit-cell parametersa= 63.7,b= 68.8,c= 69.7 Å, α = 60.6, β = 87.0, γ = 68.1°. Assuming the presence of two protein molecules per asymmetric unit, the solvent content was estimated to be 49.5%.

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