Browse
Submit Data
Databases
API
Help

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Purification, crystallization and preliminary X-ray diffraction analysis of a plant subtilase.

ABSTRACT: The subtilase SBT3 from Solanum lycopersicum (tomato) was purified from a tomato cell culture and crystallized using the sitting-drop vapour-diffusion method. A native data set was collected to 2.5 A resolution at 100 K using synchrotron radiation. For experimental phasing, CsCl-derivative and tetrakis(acetoxymercuri)methane (TAMM) derivative crystals were employed for MIRAS phasing. Three caesium sites and one TAMM site were identified, which allowed solution of the structure.

SUBMITTER: Rose R

PROVIDER: S-EPMC2675601 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Purification, crystallization and preliminary X-ray diffraction analysis of a plant subtilase.

Rose Rolf R Huttenlocher Franziska F Cedzich Anna A Kaiser Markus M Schaller Andreas A Ottmann Christian C

Acta crystallographica. Section F, Structural biology and crystallization communications 20090428 Pt 5

The subtilase SBT3 from Solanum lycopersicum (tomato) was purified from a tomato cell culture and crystallized using the sitting-drop vapour-diffusion method. A native data set was collected to 2.5 A resolution at 100 K using synchrotron radiation. For experimental phasing, CsCl-derivative and tetrakis(acetoxymercuri)methane (TAMM) derivative crystals were employed for MIRAS phasing. Three caesium sites and one TAMM site were identified, which allowed solution of the structure. ...[more]

PMID: 19407393

Similar Datasets

Purification, crystallization and preliminary X-ray diffraction analysis of the plant Rho protein ROP5.

Project description:The small G protein ROP5 from the model plant Arabidopsis thaliana was purified and crystallized using the hanging-drop vapour-diffusion method. ROP5 crystals were obtained using PEG 3000 as precipitant and belong to space group P2(1). A data set was collected to 1.53 A resolution using synchrotron radiation at 100 K. A clear molecular-replacement solution was found using ROP4-GDP of the ROP4-GDP-PRONE8 complex as the search model.

| S-EPMC2344096 | biostudies-literature

Purification, crystallization and preliminary X-ray diffraction analysis of human chondroadherin.

Project description:Chondroadherin is a cartilage matrix protein that is known to mediate the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats flanked by cysteine-rich domains at the N- and C-terminal ends. Recombinant human chondroadherin was crystallized using the sitting-drop vapour-diffusion method. The crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 56.4, b = 111.3, c = 128.5 A, beta = 92.2, and are most likely to contain four molecules in the asymmetric unit. The crystals diffracted to at least 2.3 A using synchrotron radiation, but structure determination using molecular replacement has so far been unsuccessful.

| S-EPMC2496858 | biostudies-literature

Purification, crystallization and preliminary X-ray diffraction of human S100A15.

Project description:Human S100A15 is a novel member of the S100 family of EF-hand calcium-binding proteins and was recently identified in psoriasis, where it is significantly upregulated in lesional skin. The protein is implicated as an effector in calcium-mediated signal transduction pathways. Although its biological function is unclear, the association of the 11.2 kDa S100A15 with psoriasis suggests that it contributes to the pathogenesis of the disease and could provide a molecular target for therapy. To provide insight into the function of S100A15, the protein was crystallized to visualize its structure and to further the understanding of how the many similar calcium-binding mediator proteins in the cell distinguish their cognate target molecules. The S100A15 protein has been cloned, expressed and purified to homogeneity and produced two crystal forms. Crystals of form I are triclinic, with unit-cell parameters a = 33.5, b = 44.3, c = 44.8 angstroms, alpha = 71.2, beta = 68.1, gamma = 67.8 degrees and an estimated two molecules in the asymmetric unit, and diffract to 1.7 angstroms resolution. Crystals of form II are monoclinic, with unit-cell parameters a = 82.1, b = 33.6, c = 52.2 angstroms, beta = 128.2 degrees and an estimated one molecule in the asymmetric unit, and diffract to 2.0 angstroms resolution. This structural analysis of the human S100A15 will further aid in the phylogenic comparison between the other members of the S100 protein family, especially the highly homologous paralog S100A7.

| S-EPMC2219979 | biostudies-literature

Purification, crystallization and preliminary X-ray diffraction analysis of ThiM from Staphylococcus aureus.

Project description:ThiM [5-(hydroxyethyl)-4-methylthiazole kinase; EC 2.7.1.50] from Staphylococcus aureus is an essential enzyme of thiamine or vitamin B(1) metabolism and has been crystallized by the vapour-diffusion method. The crystals belonged to the primitive space group P1, with unit-cell parameters a = 62.06, b = 62.40, c = 107.82?Å, ? = 92.25, ? = 91.37, ? = 101.48° and six protomers in the unit cell, corresponding to a packing parameter V(M) of 2.3?Å(3)?Da(-1). Diffraction data were collected to 2.1?Å resolution using synchrotron radiation. The phase problem was solved by molecular replacement.

| S-EPMC3080155 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray diffraction analysis of nurse shark ?2-microglobulin.

Project description:?(2)-Microglobulin (?(2)m) is an essential subunit of the major histocompatibility complex (MHC) class I molecule that helps to stabilize the structure of peptide-MHC I (pMHC I). It is also one of the typical immunoglobulin superfamily (IgSF) molecules in the adaptive immune system (AIS). Sharks belong to the cartilaginous fish, which are the oldest jawed vertebrate ancestors with an AIS to exist in the world. Thus, the study of cartilaginous fish ?(2)m would help in understanding the evolution of IgSF molecules. In order to demonstrate this, ?(2)m from a cartilaginous fish, nurse shark (Ginglymostoma cirratum), was expressed, refolded, purified and crystallized. Diffraction data were collected to a resolution of 2.3 Å. The crystal belonged to space group P3(2)21, with unit-cell parameters a = b = 88.230, c = 67.146 Å. The crystal structure contained two molecules in the asymmetric unit. The results will provide structural information for study of the evolution of ?(2)m and IgSF in the AIS.

| S-EPMC3325820 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray diffraction analysis of grass carp beta2-microglobulin.

Project description:Beta(2)-microglobulin (beta(2)m) is an essential subunit of MHC I molecules; it stabilizes the structure of MHC I and plays a pivotal role in coreceptor recognition. To date, structures of beta(2)m have been solved for three different mammals: human, mouse and cattle. In order to illuminate the molecular evolutionary origin of beta2m, an understanding of its structure in lower vertebrates becomes important. Here, grass carp (Ctenopharyngodon idellus) beta(2)m (Ctid-beta(2)m) was expressed, purified and crystallized. Diffraction data were collected to a resolution of 2.5 A. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 38.72, b = 40.65, c = 71.12 A. The Matthews coefficient and the solvent content were calculated to be 2.56 A Da(-1) and 52.07%, respectively, for one molecule per asymmetric unit. The structure has been solved by molecular replacement using monomeric human beta(2)m as a model.

| S-EPMC2374163 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray diffraction analysis of Bifidobacterium adolescentis xylose isomerase.

Project description:Xylose isomerase (EC 5.3.1.5) is a key enzyme in xylose metabolism which is industrially important for the transformation of glucose and xylose into fructose and xylulose, respectively. The Bifidobacterium adolescentis xylA gene (NC_008618.1) encoding xylose isomerase (XI) was cloned and the enzyme was overexpressed in Escherichia coli. Purified recombinant XI was crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol 3350 as the precipitating agent. A complete native data set was collected to 1.7?Å resolution using a synchrotron-radiation source. The crystals belonged to the orthorhombic space group P21212, with unit-cell parameters a = 88.78, b = 123.98, c = 78.63?Å.

| S-EPMC3660909 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray diffraction analysis of Deg5 from Arabidopsis thaliana.

Project description:Arabidopsis thaliana Deg5 is an ATP-independent serine protease which resides on the luminal side of the thylakoid in chloroplasts. Deg5 and another Deg/HtrA-family protease, Deg8, have a synergistic function in the turnover of the D1 protein of photosystem II (PSII), which is prone to damage arising from high light exposure. An inactive mutant of the protein, Deg5(S266A), was overexpressed in Escherichia coli. After purification and crystallization, crystals that diffracted to 2.6?Å resolution were obtained. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 109.1, b = 126.0, c = 83.3?Å, ? = 102.9°, and contained three molecules in the asymmetric unit. The calculated Matthews coefficient and solvent content were 3.0?Å(3)?Da(-1) and 59.0%, respectively.

| S-EPMC3388936 | biostudies-literature

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of recombinant human fumarase.

Project description:Human fumarase (HsFH) is a well-known citric acid cycle enzyme and is therefore a key component in energy metabolism. Genetic studies on human patients have shown that polymorphisms in the fumarase gene are responsible for diseases such as hereditary leiomyomatosis and renal cell cancer. As a first step in unravelling the molecular basis of the mechanism of fumarase deficiency in genetic disorders, the HsFH gene was cloned in pET-28a, heterologously expressed in Escherichia coli, purified by nickel-affinity chromatography and crystallized using the vapour-diffusion technique. X-ray diffraction experiments were performed at a synchrotron source and the structure was solved at 2.1?Å resolution by molecular replacement.

| S-EPMC3943092 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray diffraction analysis of galactokinase from Pyrococcus horikoshii.

Project description:Galactokinase (EC 2.7.1.6) catalyzes the ATP-dependent phosphorylation of alpha-D-galactose to alpha-D-galactose-1-phosphate, in an additional metabolic branch of glycolysis. The apo-form crystal structure of the enzyme has not yet been elucidated. Crystals of galactokinase from Pyrococcus horikoshii were prepared in both the apo form and as a ternary complex with alpha-D-galactose and an ATP analogue. Diffraction data sets were collected to 1.24 A resolution for the apo form and to 1.7 A for the ternary complex form using synchrotron radiation. The apo-form crystals belong to space group C2, with unit-cell parameters a = 108.08, b = 38.91, c = 81.57 A, beta = 109.8 degrees. The ternary complex form was isomorphous with the apo form, except for the length of the a axis. The galactokinase activity of the enzyme was confirmed and the kinetic parameters at 323 K were determined.

| S-EPMC2150956 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data