Crystallization and preliminary X-ray diffraction studies of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus

1999 ◽  
Vol 55 (7) ◽  
pp. 1353-1355 ◽  
Author(s):  
C. Charron ◽  
F. Talfournier ◽  
M. N. Isupov ◽  
G. Branlant ◽  
J. A. Littlechild ◽  
...  
Keyword(s):  
Diffusion Method ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Data Set ◽  
Hyperthermophilic Archaeon ◽  
X Ray ◽  
Cell Dimensions ◽  
Methanothermus Fervidus ◽  
Unit Cell Dimensions

The homotetrameric holo-D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus has been crystallized in the presence of NADP+ using the hanging-drop vapour-diffusion method. Crystals grew from a solution containing 2-methyl-2,4-pentanediol and magnesium acetate. A native data set has been collected to 2.1 Å using synchrotron radiation and cryocooling. Diffraction data have been processed in the orthorhombic system (space group P21212) with unit-cell dimensions a = 136.7, b = 153.3, c = 74.9 Å and one tetramer per asymmetric unit.

Crystallization and preliminary X-ray analysis of the Escherichia coli UDP-MurNAc-tripeptide D-alanyl-D-alanine-adding enzyme (MurF)

1999 ◽  
Vol 55 (12) ◽  
pp. 2033-2034 ◽  
Author(s):  
Youwei Yan ◽  
Sanjeev Munshi ◽  
Ying Li ◽  
Kelly Ann D. Pryor ◽  
Frank Marsilio ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Data Set ◽  
Solvent Content ◽  
X Ray ◽  
Protein Mass ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Crystal Volume

Crystals of the Escherichia coli UDP-MurNAc-tripeptide D-Ala-D-Ala-adding protein (MurF), which catalyzes the formation of the last metabolite of the bacterial cell-wall building block, have been grown in hanging-drop vapor-diffusion trials using PEG 8K as a precipitating agent. The crystals belong to hexagonal space group P61 or P65, with unit-cell dimensions a = b = 74, c = 425 Å. The asymmetric unit contains two molecules, with a crystal volume per protein mass (Vm ) of 3.4 Å3 Da−1 and a solvent content of about 64% by volume. A native data set to 2.8 Å resolution has been obtained from a frozen crystal using a synchrotron X-ray source.

scholarly journals Crystallization and preliminary X-ray diffraction analysis ofBacillus subtilisYwfE, anL-amino-acid ligase

2012 ◽  
Vol 68 (2) ◽  
pp. 203-206 ◽  
Author(s):  
Takeo Tsuda ◽  
Tomomi Suzuki ◽  
Shuichi Kojima
Keyword(s):  
Amino Acid ◽  
Diffusion Method ◽  
Dependent Manner ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters

Bacillus subtilisYwfE, an L-amino-acid ligase, catalyzes the formation of an α-dipeptide from L-amino acids in an ATP-dependent manner. In order to elucidate the substrate-recognition mode and the reaction mechanism of this ligase, native and selenomethionine-derivatized (SeMet) crystals of YwfE in the presence of ADP, MgCl2and the dipeptide L-Ala-L-Gln were obtained using the hanging-drop vapour-diffusion method. These crystals diffracted to 1.9 and 2.8 Å resolution, respectively. Preliminary SAD phase calculations using the data set from the SeMet crystal suggested that the crystal belonged to the hexagonal space groupP6522, with unit-cell parametersa=b= 90.85,c = 250.31 Å, and contained one molecule in the asymmetric unit with a solvent content of 57.3%.

Crystallization and preliminary X-ray analysis of the 6-phospho-α-glucosidase from Bacillus subtilis

1999 ◽  
Vol 55 (6) ◽  
pp. 1212-1214 ◽  
Author(s):  
Annabelle Varrot ◽  
Hiroki Yamamoto ◽  
Junichi Sekiguchi ◽  
John Thompson ◽  
Gideon J. Davies
Keyword(s):  
Bacillus Subtilis ◽  
Single Molecule ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Phosphotransferase System ◽  
X Ray ◽  
Cell Dimensions ◽  
Hanging Drop Method ◽  
Unit Cell Dimensions

6-Phospho-α-glucosidase (GlvA) is the protein involved in the dissimilation of α-glycosides accumulated via a phosphoenolpyruvate-dependent maltose phosphotransferase system (PEP-PTS) in Bacillus subtilis. The purified enzyme has been crystallized in a form suitable for X-ray diffraction analysis. Thin rod-like crystals have been grown by the hanging-drop method in the presence of manganese and NAD. They diffract beyond 2.2 Å using synchrotron radiation and belong to the space group I222 (or its enantiomorph) with unit-cell dimensions a = 83.26, b = 102.56, c = 145.31 Å and contain a single molecule of GlvA in the asymmetric unit.

Crystallization and preliminary X-ray diffraction analysis of malic enzyme from pigeon liver

1999 ◽  
Vol 55 (11) ◽  
pp. 1930-1932 ◽  
Author(s):  
Li-Chu Tsai ◽  
Chen-Chin Kuo ◽  
Wei-Yuan Chou ◽  
Gu-Gang Chang ◽  
Hanna S. Yuan
Keyword(s):  
Malic Enzyme ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cells ◽  
Unit Cell Dimensions ◽  
Pigeon Liver

Recombinant pigeon-liver malic enzyme was expressed in Escherichia coli and purified to homogeneity. Two different crystal forms were grown by the hanging-drop vapour-diffusion method. Both types of crystals belong to the tetragonal space group P4222, with unit-cell dimensions a = b = 163.8, c = 174.3 Å for the octahedral crystals and a = b = 124.5, c = 179.2 Å for the rod-like crystals. X-ray diffraction data were collected at 100 K using a synchrotron-radiation X-ray source. The Matthews parameter suggests that there are four and two molecules per asymmetric unit for the larger and the smaller tetragonal unit cells, respectively.

Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus

1998 ◽  
Vol 54 (1) ◽  
pp. 127-128 ◽  
Author(s):  
Takanori Kumagai ◽  
Kengo Muta ◽  
Yasuyuki Matoba ◽  
Yoshiaki Kawano ◽  
Nobuo Kamiya ◽  
...  
Keyword(s):  
Binding Protein ◽  
Diffusion Method ◽  
X Rays ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Diffraction Intensity ◽  
Data Set ◽  
X Ray ◽  
Peg 4000 ◽  
Cell Dimensions

A bleomycin-binding protein (BLMA) produced by bleomycin-producing Streptomyces verticullus was crystallized in a form suitable for X-ray diffraction analysis using the vapor-diffusion method. Crystals were grown at pH 5.7, in 0.2 M NH4 actate and 0.1 M Na acetate, using 30% PEG 4000 as a precipitant. They belong to the orthorhombic system, with space group P21212, cell dimensions a = 54.90, b = 67.94, c = 35.60 Å, and one BLMA molecule in the asymmetric unit. The crystals diffract X-rays well and the diffraction intensity data was collected up to 1.5 Å resolution with a merging R value of 0.054 at beamline 6B of the Photon Factory. The diffraction data set is 94% complete.

Purification, crystallization and preliminary X-ray crystallographic analysis of recombinant murine Golgi mannosidase IA, a class I α-mannosidase involved in Asn-linked oligosaccharide maturation

1999 ◽  
Vol 55 (2) ◽  
pp. 571-573 ◽  
Author(s):  
Francois Vallée ◽  
Anita Lal ◽  
Kelley W. Moremen ◽  
P. Lynne Howell
Keyword(s):  
Transmembrane Domain ◽  
Crystallographic Analysis ◽  
Class I ◽  
Diffusion Method ◽  
Type Ii ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Golgi mannosidase IA is a class I α-mannosidase which catalyzes the conversion of Man9GlcNAc2 or Man8GlcNAc2 oligosaccharide substrates to Man5GlcNAc2 during the maturation of Asn-linked oligosaccharides. The enzyme is a type II membrane protein, and a recombinant form of mannosidase IA from mouse, lacking the transmembrane domain, has been expressed in Pichia pastoris, purified to homogeneity and crystallized by the hanging-drop vapor-diffusion method. The crystals grow as thin rods, with unit-cell dimensions a = 54.9, b = 135.01, c = 69.9 Å. The crystals exhibit the symmetry of space group P2221 and diffract to 2.8 Å resolution. The asymmetric unit contains one monomer (∼53 kDa) and has a solvent content of 59%.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of the effector protein PevD1 fromVerticillium dahliae

2012 ◽  
Vol 68 (7) ◽  
pp. 802-805 ◽  
Author(s):  
Lei Han ◽  
Zheng Liu ◽  
Xinqi Liu ◽  
Dewen Qiu
Keyword(s):  
Pathogenic Fungus ◽  
Sodium Formate ◽  
Diffusion Method ◽  
Effector Protein ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Dispersion Method ◽  
Data Set ◽  
X Ray ◽  
Anomalous Signal

The effector protein PevD1 from the pathogenic fungusVerticillium dahliaewas purified and crystallized using the hanging-drop vapour-diffusion method. Native crystals appeared in a solution consisting of 4.0 Msodium formate. A native data set was collected at 1.9 Å resolution at 100 K using an in-house X-ray source. Because of the absence of useful methinione in the protein sequence, derivative crystals that contained iodine were obtained by soaking in 1.25 Mpotassium iodide, and a data set that contained anomalous signal was collected using the same X-ray facility at a wavelength of 1.54 Å. The single-wavelength anomalous dispersion method was used to successfully solve the structure based on the anomalous signal generated from iodine.

Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease–DNA complex

1999 ◽  
Vol 55 (11) ◽  
pp. 1943-1945 ◽  
Author(s):  
Nancy C. Horton ◽  
Lydia F. Dorner ◽  
Ira Schildkraut ◽  
John J. Perona
Keyword(s):  
High Energy ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Data Set ◽  
Synchrotron Source ◽  
Polyethylene Glycol 4000 ◽  
Dimeric Complexes ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Dna Complex

Crystals of the 60 kDa dimeric HincII restriction enzyme bound to a 12 base-pair dyad-symmetric duplex DNA carrying the specific 5′-GTCGAC recognition site have been obtained. Crystals grew by hanging-drop vapor diffusion from solutions containing polyethylene glycol 4000 as precipitating agent. The rod-shaped crystals belong to space group I222 (or I212121), with unit-cell dimensions a = 66.9, b = 176.7, c = 256.0 Å. There are most likely to be two dimeric complexes in the asymmetric unit. A complete native data set has been collected from a high-energy synchrotron source to a resolution of 2.5 Å at 100 K, with an R merge of 4.8%.

Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance-B (NusB) from Mycobacterium tuberculosis

2000 ◽  
Vol 56 (1) ◽  
pp. 64-66 ◽  
Author(s):  
B. Gopal ◽  
R. A. Cox ◽  
M. J. Colston ◽  
G. G. Dodson ◽  
S. J. Smerdon ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Ribosomal Rna ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Core Complex ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters

N-utilizing substance B (NusB) is a protein which forms part of a complex assembly in transcriptional antitermination in Mycobacterium tuberculosis. It forms a heterodimer with the product of the NusE gene (identical to the ribosomal protein S10) and mediates the process of transcriptional antitermination by forming the core complex with the nut site of the ribosomal RNA along with other protein factors. NusB has been cloned and overexpressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. The space group is P212121, with unit-cell parameters a = 46.6, b = 64.2, c = 90.1 Å. A native data set complete to 1.6 Å resolution has been collected from a single crystal.

Crystallization and preliminary X-ray analysis of β-amylase from Bacillus polymyxa

1999 ◽  
Vol 55 (4) ◽  
pp. 898-900
Author(s):  
Takashi Yamane ◽  
Hiroshi Tasaki ◽  
Fusako Matsumoto ◽  
Atsuo Suzuki ◽  
Nobuyuki Uozumi ◽  
...  
Keyword(s):  
Diffusion Method ◽  
Bacillus Polymyxa ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Dimensions ◽  
Protein Molecules ◽  
Density Map ◽  
Electron Density Map

A truncated β-amylase (E.C. 3.2.1.2) from Bacillus polymyxa has been crystallized using the hanging-drop vapour-diffusion method at 277 K. The crystals belong to the orthorhombic space group P212121 with cell dimensions a = 64.6, b = 141.9, c = 155.1 Å and diffract to 2.5 Å resolution. The asymmetric unit containing three protein molecules was derived from an electron-density map calculated at 4 Å resolution using MIR phases. This gives a Vm value of 2.36 Å3 Da−1.

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