Crystallization and preliminary X-ray analysis of human thioredoxin peroxidase-B from red blood cells

1999 ◽  
Vol 55 (2) ◽  
pp. 536-538 ◽  
Author(s):  
Ewald Schröder ◽  
Michail N. Isupov ◽  
Anouska Naran ◽  
Jennifer A. Littlechild
Keyword(s):  
Polyethylene Glycol ◽  
Synchrotron Radiation ◽  
Blood Cells ◽  
Data Sets ◽  
Polyethylene Glycol 400 ◽  
Crystal Forms ◽  
X Ray ◽  
Vapour Diffusion ◽  
Thioredoxin Peroxidase ◽  
Orthorhombic Crystals

Two different crystal forms of human thioredoxin peroxidase-B have been grown by vapour diffusion using polyethylene glycol 400 as a precipitant. Monoclinic P21 crystals were grown from freshly purified protein, whilst orthorhombic P212121 crystals were grown from purified protein that had been stored in ammonium sulfate, but otherwise under the same conditions. The diffraction from both crystal forms was observed to extend to beyond 2.0 Å resolution using synchrotron radiation. Complete native data sets to 1.8 and 3.7 Å have been collected from the monoclinic and orthorhombic crystals, respectively.

scholarly journals Monitoring protein precipitates by in-house X-ray powder diffraction

2013 ◽  
Vol 28 (S2) ◽  
pp. S458-S469 ◽  
Author(s):  
Kenny Ståhl ◽  
Christian G. Frankær ◽  
Jakob Petersen ◽  
Pernille Harris
Keyword(s):  
Powder Diffraction ◽  
Protein Crystal ◽  
Data Sets ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Parameters ◽  
X Ray Scattering ◽  
Source Organism ◽  
Peak Asymmetry ◽  
Overlapping Peaks

Powder diffraction from protein powders using in-house diffractometers is an effective tool for identification and monitoring of protein crystal forms and artifacts. As an alternative to conventional powder diffractometers a single crystal diffractometer equipped with an X-ray micro-source can be used to collect powder patterns from 1 µl samples. Using a small-angle X-ray scattering (SAXS) camera it is possible to collect data within minutes. A streamlined program has been developed for the calculation of powder patterns from pdb-coordinates, and includes correction for bulk-solvent. A number of such calculated powder patterns from insulin and lysozyme have been included in the powder diffraction database and successfully used for search-match identification. However, the fit could be much improved if peak asymmetry and multiple bulk-solvent corrections were included. When including a large number of protein data sets in the database some problems can be foreseen due to the large number of overlapping peaks in the low-angle region, and small differences in unit cell parameters between pdb-data and powder data. It is suggested that protein entries are supplied with more searchable keywords as protein name, protein type, molecular weight, source organism etc. in order to limit possible hits.

scholarly journals Expression, purification, crystallization and preliminary X-ray analysis of tannase fromLactobacillus plantarum

2013 ◽  
Vol 69 (4) ◽  
pp. 456-459 ◽  
Author(s):  
Mingbo Wu ◽  
Xiaohong Peng ◽  
Hua Wen ◽  
Qin Wang ◽  
Qianming Chen ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Gallic Acid ◽  
Diffusion Method ◽  
Ester Bond ◽  
Asymmetric Unit ◽  
Data Set ◽  
X Ray ◽  
Vapour Diffusion ◽  
Serine Esterases ◽  
Hydrolysis Of

Tannase catalyses the hydrolysis of the galloyl ester bond of tannins to release gallic acid. It belongs to the serine esterases and has wide applications in the food, feed, beverage, pharmaceutical and chemical industries. The tannase fromLactobacillus plantarumwas cloned, expressed and purified. The protein was crystallized by the sitting-drop vapour-diffusion method with microseeding. The crystals belonged to space groupP1, with unit-cell paramtersa= 46.5,b= 62.8,c= 83.8 Å, α = 70.4, β = 86.0, γ = 79.4°. Although the enzyme exists mainly as a monomer in solution, it forms a dimer in the asymmetric unit of the crystal. The crystals diffracted to beyond 1.60 Å resolution using synchrotron radiation and a complete data set was collected to 1.65 Å resolution.

Charge Density of L-Alanyl-glycyl-L-alanine Based on X-Ray Data Collection Periods from 4 to 130 Hours

2007 ◽  
Vol 62 (5) ◽  
pp. 696-704 ◽  
Author(s):  
Diana Förster ◽  
Armin Wagner ◽  
Christian B. Hübschle ◽  
Carsten Paulmann ◽  
Peter Luger
Keyword(s):  
Synchrotron Radiation ◽  
Low Temperature ◽  
Charge Density ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Atomic Properties ◽  
Multipole Refinement ◽  
Refinement Strategy ◽  
Experimental Charge Density

Abstract The charge density of the tripeptide L-alanyl-glycyl-L-alanine was determined from three X-ray data sets measured at different experimental setups and under different conditions. Two of the data sets were measured with synchrotron radiation (beamline F1 of Hasylab/DESY, Germany and beamline X10SA of SLS, Paul-Scherer-Institute, Switzerland) at temperatures around 100 K while a third data set was measured under home laboratory conditions (MoKα radiation) at a low temperature of 20 K. The multipole refinement strategy to derive the experimental charge density was the same in all cases, so that the obtained charge density properties could directly be compared. While the general analysis of the three data sets suggested a small preference for one of the synchrotron data sets (Hasylab F1), a comparison of topological and atomic properties gave in no case an indication for a preference of any of the three data sets. It follows that even the 4 h data set measured at the SLS performed equally well compared to the data sets of substantially longer exposure time.

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 Overexpression, crystallization and preliminary X-ray crystallographic analysis of the ectoine hydroxylase fromSphingopyxis alaskensis

2014 ◽  
Vol 70 (4) ◽  
pp. 493-496 ◽  
Author(s):  
Astrid Hoeppner ◽  
Nils Widderich ◽  
Erhard Bremer ◽  
Sander H. J. Smits
Keyword(s):  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Oxidative Decarboxylation ◽  
Expression And Purification ◽  
Crystal Forms ◽  
X Ray ◽  
Mononuclear Iron ◽  
Vapour Diffusion ◽  
Purification Protocol

The ectoine hydroxylase (EctD) is a member of the non-haem-containing iron(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. Its mononuclear iron centre is a prerequisite for the activity of this enzyme and promotes the O2-dependent oxidative decarboxylation of 2-oxoglutarate, which is coupled to a two-electron oxidation of the substrate ectoine to yield 5-hydroxyectoine. An expression and purification protocol for the EctD enzyme fromSphingopyxis alaskensiswas developed and the protein was crystallized using the sitting-drop vapour-diffusion method. This resulted in two different crystal forms, representing the apo and iron-bound forms of the enzyme.

Synchrotron radiation study of yttria-stabilized zirconia, Zr0.758Y0.242O1.879

1999 ◽  
Vol 55 (5) ◽  
pp. 726-735 ◽  
Author(s):  
N. Ishizawa ◽  
Y. Matsushima ◽  
M. Hayashi ◽  
M. Ueki
Keyword(s):  
Synchrotron Radiation ◽  
Single Crystal ◽  
Yttria Stabilized Zirconia ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Stabilized Zirconia ◽  
X Ray ◽  
Ideal Position ◽  
Fluorite Type ◽  
The Ideal

The fluorite-related cubic structure of yttria-stabilized zirconia, Zr0.75 8Y0.24 2O1.87 9, has been studied by single-crystal X-ray diffraction using synchrotron radiation and by EXAFS. Two diffraction data sets obtained at X-ray energies of 512 and 10 eV below the Y K edge revealed that in the average structure Zr atoms are displaced from the origin of the space group Fm3¯m along 〈111〉 by 0.19 Å, while Y atoms reside at the origin. Approximately 48% of the O atoms occupy the ideal position in the fluorite-type structure, while 43% of O atoms are displaced from the ideal position along 〈001〉 by 0.31 Å. The remaining 9% of O atoms are presumably sited at interstitial positions. Local structures around Zr and Y are investigated by combining the results of single-crystal X-ray diffraction and EXAFS studies.

Crystallization and preliminary X-ray analysis of recombinant full-length human m-calpain

2000 ◽  
Vol 56 (1) ◽  
pp. 73-75 ◽  
Author(s):  
Hajime Masumoto ◽  
Kazuhiro Nakagawa ◽  
Shota Irie ◽  
Hiroyuki Sorimachi ◽  
Koichi Suzuki ◽  
...  
Keyword(s):  
Full Length ◽  
Data Sets ◽  
Cysteine Proteinases ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Monoclinic Crystal ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Parameters ◽  
Cooling Conditions

m-Calpain constitutes the prototype of the superfamily of neutral calcium-activated cysteine proteinases. It is a heterodimer consisting of an 80 and a 30 kDa subunit. Recombinant full-length human m-calpain has been crystallized using macro-seeding techniques and vapour-diffusion methods. Two different monoclinic crystal forms (space group P21) were obtained from a solution containing polyethylene glycol (MW = 10 000) as a pecipitating agent. Complete data sets have been collected to 2.3 and 3.0 Å resolution using cryo-cooling conditions and synchrotron radiation. The unit-cell parameters are a = 64.86, b = 133.97, c = 78.00 Å, β = 102.43° and a = 51.80, b = 171.36, c = 64.66 Å, β = 94.78°, respectively. The Vm values indicate that there is one heterodimer in each asymmetric unit.

Expression, purification, crystallization and preliminary X-ray analysis of the κ-carrageenase from Pseudoalteromonas carrageenovora

1999 ◽  
Vol 55 (4) ◽  
pp. 918-920 ◽  
Author(s):  
Gurvan Michel ◽  
Tristan Barbeyron ◽  
Didier Flament ◽  
Thierry Vernet ◽  
Bernard Kloareg ◽  
...  
Keyword(s):  
Polyethylene Glycol ◽  
Unit Cell ◽  
Recombinant Form ◽  
Diffusion Method ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Vapour Diffusion

A recombinant form of His-tagged κ-carrageenase from Pseudoalteromonas carrageenovora has been expressed, purified and crystallized. Crystals have been obtained by the vapour-diffusion method using polyethylene glycol (Mr = 4000) as a precipitant. These crystals belong to the space group P212121, with unit-cell parameters a  =  58.2, b  =  62.8, c  =  77.9 Å, and diffract to 2.2 Å resolution on a rotating-anode X-ray source.

scholarly journals Crystallization and preliminary X-ray analysis of the C-terminal fragment of PorM, a subunit of thePorphyromonas gingivalistype IX secretion system

2015 ◽  
Vol 71 (1) ◽  
pp. 71-74 ◽  
Author(s):  
Julien Stathopulos ◽  
Christian Cambillau ◽  
Eric Cascales ◽  
Alain Roussel ◽  
Philippe Leone
Keyword(s):  
Escherichia Coli ◽  
Synchrotron Radiation ◽  
Limited Proteolysis ◽  
Bacterial Pathogen ◽  
Secretion System ◽  
Data Sets ◽  
X Ray ◽  
A Subunit ◽  
Periplasmic Domain ◽  
Type Ix Secretion System

PorM is a membrane protein involved in the assembly of the type IX secretion system (T9SS) fromPorphyromonas gingivalis, a major bacterial pathogen responsible for periodontal disease in humans. The periplasmic domain of PorM was overexpressed inEscherichia coliand purified. A fragment of the purified protein was obtained by limited proteolysis. Crystals of this fragment belonged to the tetragonal space groupP43212. Native and MAD data sets were recorded to 2.85 and 3.1 Å resolution, respectively, using synchrotron radiation.

scholarly journals SynchLink: an iOS app for ISPyB

2014 ◽  
Vol 47 (5) ◽  
pp. 1781-1783 ◽  
Author(s):  
Helen Mary Ginn ◽  
Ghita Kouadri Mostefaoui ◽  
Karl Erik Levik ◽  
Jonathan Mark Grimes ◽  
Martin Austin Walsh ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Real Time ◽  
Computer Hardware ◽  
Data Sets ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Data Acquisition Software ◽  
Efficient Access ◽  
Structure Solution ◽  
The Impact

The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X-ray detectors, computer hardware and automation methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information-rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now providedviaan iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.

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