Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Preliminary crystallographic analysis of RraB from Escherichia coli.

ABSTRACT: RraB, an inhibitor of the essential endoribonuclease RNE in Escherichia coli, is essential in regulating the abundance of RNA by directly interacting with RNE. In this study, RraB from E. coli was cloned, expressed, purified and crystallized. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.59, b = 58.34, c = 156.95?Å. X-ray diffraction data were collected to a resolution of 2.9?Å. Analysis of the native Patterson map revealed a peak of ?37% the height of the origin peak in the ? = 0.5 Harker section, suggesting twofold noncrystallographic symmetry parallel to the b crystallographic axis. The Matthews coefficient and the solvent content were estimated to be 4.09?Å(3)?Da(-1) and 69.94%, respectively, assuming the presence of two molecules in the asymmetric unit.

SUBMITTER: Shen H

PROVIDER: S-EPMC3818050 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Preliminary crystallographic analysis of RraB from Escherichia coli.

Shen Hui H Liu Huihui H Wang Hong H Teng Maikun M Li Xu X

Acta crystallographica. Section F, Structural biology and crystallization communications 20131030 Pt 11

RraB, an inhibitor of the essential endoribonuclease RNE in Escherichia coli, is essential in regulating the abundance of RNA by directly interacting with RNE. In this study, RraB from E. coli was cloned, expressed, purified and crystallized. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.59, b = 58.34, c = 156.95 Å. X-ray diffraction data were collected to a resolution of 2.9 Å. Analysis of the native Patterson map revealed a peak of ∼37% the height of the ...[more]

PMID: 24192366

Similar Datasets

Cloning, purification, crystallization and preliminary crystallographic analysis of LsrR from Escherichia coli.

Project description:In Escherichia coli, the lsr operon is composed of six genes lsrACDBFG which regulate uptake and modification of the signalling molecule AI-2. LsrR is a repressor of the lsr operon and itself, which can bind phospho-AI-2 and be released from the promoter region of the operon and thus activate gene expression. LsrR fused with an HHHHHH sequence at the C-terminus was expressed, purified and crystallized in order to determine its structure and elucidate the molecular mechanism of repression. The crystal belonged to space group I222, with unit-cell parameters a=79.84, b=116.65, c=186.04 A, and was estimated to contain two protein molecules per asymmetric unit.

| S-EPMC2917289 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of YgjG from Escherichia coli.

Project description:Putrescine, one of the polyamines that are found in virtually all living organisms, has been implicated as an important biological material. The protein YgjG is involved in the putrescine-degradation pathway in Escherichia coli. The enzyme is a putrescine:2-oxoglutarate aminotransferase that belongs to the class III aminotransferases. In this study, YgjG from E. coli was overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. Diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 121.1, b = 129.5, c = 131.3 Å, and is estimated to contain four molecules of YgjG per asymmetric unit.

| S-EPMC3433200 | biostudies-literature

Expression, purification, crystallization and preliminary crystallographic analysis of spermidine acetyltransferase from Escherichia coli.

Project description:The spermidine acetyltransferase (SAT) from Escherichia coli catalyses the transfer of acetyl groups from acetyl-CoA to spermidine. SAT has been expressed and purified from E. coli. SAT was crystallized by the sitting-drop vapour-diffusion method to obtain a more detailed insight into the molecular mechanism. Preliminary X-ray diffraction studies revealed that the crystals diffracted to 2.5 Å resolution and belonged to the cubic space group P23, with unit-cell parameters a = b = c = 148.7 Å. They contained four molecules per asymmetric unit.

| S-EPMC3729165 | biostudies-other

Crystallization and preliminary crystallographic analysis of tRNA (m(7)G46) methyltransferase from Escherichia coli.

Project description:Transfer RNA (tRNA) (m(7)G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-L-methionine (SAM) as the methyl-group donor to catalyze the formation of N(7)-methylguanosine (m(7)G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His(6) tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P2(1).

| S-EPMC2494960 | biostudies-literature

Preliminary X-ray crystallographic analysis of an engineered glutamyl-tRNA synthetase from Escherichia coli.

Project description:The nature of interaction between glutamyl-tRNA synthetase (GluRS) and its tRNA substrate is unique in bacteria in that many bacterial GluRS are capable of recognizing two tRNA substrates: tRNAGlu and tRNAGln. To properly understand this distinctive GluRS-tRNA interaction it is important to pursue detailed structure-function studies; however, because of the fact that tRNA-GluRS interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure-function correlation studies must also be phylum-specific. GluRS from Thermus thermophilus and Escherichia coli, which belong to evolutionarily distant phyla, are the biochemically best characterized. Of these, only the structure of T. thermophilus GluRS is available. To fully unravel the subtleties of tRNAGlu-GluRS interaction in E. coli, a model bacterium that can also be pathogenic, determination of the E. coli GluRS structure is essential. However, previous attempts have failed to crystallize E. coli GluRS. By mapping crystal contacts of a homologous GluRS onto the E. coli GluRS sequence, two surface residues were identified that might have been hindering crystallization attempts. Accordingly, these two residues were mutated and crystallization of the double mutant was attempted. Here, the design, expression, purification and crystallization of an engineered E. coli GluRS in which two surface residues were mutated to optimize crystal contacts are reported.

| S-EPMC4089533 | biostudies-literature

Overproduction, crystallization and preliminary X-ray crystallographic analysis of Escherichia coli tRNA N6-threonylcarbamoyladenosine dehydratase.

Project description:Escherichia coli tRNA N6-threonylcarbamoyladenosine dehydratase (TcdA), previously called CsdL or YgdL, was overproduced and purified from E. coli and 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 group P2?, with unit-cell parameters a=65.4, b=96.8, c=83.3?Å, ?=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(-1) and 42.1% solvent content.

| S-EPMC4231855 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of the 16S rRNA methyltransferase RsmI from Escherichia coli.

Project description:RsmI and RsmH are AdoMet-dependent methyltransferases that are responsible for the 2'-O-methylation and N(4)-methylation of C1402 of Escherichia coli 16S rRNA, respectively. Modification of this site has been found to play a role in fine-tuning the shape and function of the P-site to increase the decoding fidelity. It is interesting to study the mechanism by which C1402 can be methylated by both RsmI and RsmH. The crystal structure of RsmH in complex with AdoMet and cytidine has recently been determined and provided some implications for N(4)-methylation of this site. Here, the purification and crystallization of RsmI as well as its preliminary crystallographic analysis are reported. Co-crystallization of RsmI with AdoMet was carried out by the sitting-drop vapour-diffusion method and X-ray diffraction data were collected to 2.60?Å resolution on beamline 1W2B at BSRF. The crystal contained three molecules per asymmetric unit and belonged to space group C2, with unit-cell parameters a = 121.9, b = 152.5, c = 54.2?Å, ? = 93.4°.

| S-EPMC4157431 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of the 23S rRNA methyltransferase RlmM (Cm2498) from Escherichia coli.

Project description:RlmM is an AdoMet-dependent methyltransferase that is responsible for 2'-O-methylation of C2498 in the peptidyl-transferase loop of bacterial 23S rRNA. This modification occurs before assembly of the 50S ribosomal subunit, and lack of C2498 methylation can cause a slight reduction in bacterial fitness. Here, the purification and crystallization of RlmM from Escherichia coli as well as its preliminary crystallographic analysis are presented. Cocrystallization of RlmM with AdoMet was carried out and X-ray diffraction data were collected to a resolution of 2.30 Å on beamline BL17U at the SSRF. However, electron density for AdoMet cannot be observed by comprehensive crystallographic analysis, indicating that it is not bound by RlmM during the cocrystallization process. The structure was solved by molecular replacement and refinement is in progress. The crystal contained one molecule in the asymmetric unit and belonged to space group P2(1), with unit-cell parameters a = 56.07, b = 59.38, c = 54.35 Å, ? = 94.84°, which differs from the P3(1) or P3(1)21 space groups of previously reported RlmM structures (PDB entries 4auk, 4atn and 4b17).

| S-EPMC3668582 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of Z-ring-associated protein (ZapD) from Escherichia coli.

Project description:Bacterial cytokinesis is accomplished by the Z-ring, which is a polymeric structure that includes the tubulin homologue FtsZ at the division site. ZapD, a Z-ring-associated protein, directly binds to FtsZ and stabilizes the polymerization of FtsZ to form a stable Z-ring during cytokinesis. Structural analysis of ZapD from Escherichia coli was performed to investigate the mechanism of ZapD-mediated FtsZ stabilization and polymerization. ZapD was crystallized using a reservoir solution consisting of 1.5 M lithium sulfate, 0.1 M HEPES pH 7.8, 2%(v/v) polyethylene glycol 400. X-ray diffraction data were collected to 2.95 Å resolution. The crystals belonged to the hexagonal space group P64, with unit-cell parameters a = b = 109.5, c = 106.7 Å, γ = 120.0°. Two monomers were present in the asymmetric unit, resulting in a crystal volume per protein mass (VM) of 3.25 Å(3) Da(-1) and a solvent content of 62.17%.

| S-EPMC4321475 | biostudies-literature

Crystallization and preliminary crystallographic studies of UbiG, an O-methyltransferase from Escherichia coli.

Project description:UbiG, an O-methyltransferase from the ubiquinone-biosynthesis pathway in Escherichia coli, catalyzes two O-methyl transfer steps. The primary structures of the O-methyltransferase enzyme family used in ubiquinone synthesis are conserved in both prokaryotes and eukaryotes, but their tertiary structures and catalytic mechanisms are not yet known. Here, UbiG with an N-terminal hexahistidine tag was expressed and crystallized. Crystals grown by the hanging-drop vapour-diffusion method diffracted to 2.00?Å resolution and belonged to space group C121, with unit-cell parameters a = 119.8, b = 58.6, c = 40.2?Å, ? = 105.3°. Both Matthews coefficient analysis and the self-rotation function suggested the presence of one molecule per asymmetric unit in the crystal, with a solvent content of 50.52% (V(M) = 2.48?Å(3)?Da(-1)).

| S-EPMC3107154 | 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