Install SRA tool-kit on MAC OS

Download file to /Users/your_user_name/Downloads/ folder:
http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-mac64.tar.gz

Extract compressed folder:

tar -vxzf  /Users/your_user_name/Downloads/sratoolkit.current-mac64.tar.gz

Add exeacuteable to your env path:

export PATH=$PATH:/Users/your_user_name/Downloads/sratoolkit.2.6.3-mac64/bin/

Check:
which fastq-dump
This should show: 

/Users/your_user_name/Downloads/sratoolkit.2.6.3-mac64/bin//fastq-dump

For SRA tool-kit installation on other operating systems, check:
https://github.com/ncbi/sra-tools/wiki/HowTo:-Binary-Installation

Extract paired-end reads from single SRA file

for paried-end (Layout: PAIRED) data in 1 sra file, use the following command:

fastq-dump the_sra_file --split-3 -O the_output_directory

This will give you 2 (or 3) fastq files:
file_1.fastq - mate parie forward strand
file_2.fastq - mate pair reverse strand
file.fastq - reads without mate pair.

Remeber to use most up-to-date SRA took kit, it will reduce a lot of problems:
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software