Computational protocol: Structural and kinetic analysis of an MsrA–MsrB fusion protein from Streptococcus pneumoniae

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Protocol publication

[…] The crystal structure of SpMsrAB was determined by the SAD method. Searching of 12 selenium sites and calculation of phase were carried out with the SOLVE (; ). The first model was built into 2.7 Å resolution electron density map by using Coot (). After refinement with CNS (), the resolution was improved to 2.4 Å. Final refinement, after including a hexa-peptide and solvents, resulted in R and Rfree values of 23.9% and 28.2% (for a 10% data sample) respectively. Data collection and refinement statistics are summarized in . The atomic co-ordinates and structure factors for the SpMsrAB have been deposited in the Protein Data Bank with the accession code 3E0M. A crystal structure of BsMsrB was also determined (; ) and has been deposited (3E0O). The Protein Data Bank accession codes for other Msr proteins discussed in this article are as follows: BtMsrA (1FVA), EcMsrA (1FF3), MtMsrA (1NWA), NmMsrA (3BQE, 3BQF, 3BQH), PtMsrA (2J89), BsMsrB (1XM0), BpMsrB (3CEZ, 3CXK) and NgMsrB (1L1D). […]

Pipeline specifications

Software tools Coot, CNS
Application Protein structure analysis
Organisms Streptococcus pneumoniae
Chemicals Hydrogen, Methionine