Computational protocol: Structure and Mechanism of the Bifunctional CinA Enzyme from Thermus thermophilus*

Similar protocols

Protocol publication

[…] Details of data collection and refinement statistics are given in . The data sets were processed by automated pipeline implemented in XIA2 () using XDS () and AIMLESS (). The unliganded (“native” in ) TtCinA structure was solved by molecular replacement using PHASER () by finding a unique solution (log likelihood gain, −263; translation function Z score, −10.5) when two dimers, one each of two different CinA domain structures (Protein Data Bank entries 2A92 and 3KBQ) were placed. The majority of the model was built using AUTOBUILD () implemented within PHENIX (). Model building was completed manually using Coot () and refined using phenix.refine () and REFMAC (). The ligand-bound structures of TtCinA were refined using the native structure as a starting model. Clear densities for NCN, ADP-ribose, ATP, and AMP were identified in their respective (Fo − Fc) maps. Apart from docking of the ligands, which was carried out manually in Coot, only minor, manual adjustments to each structure were required. The structures were validated using Molprobity () and PROCHECK (). Coordinates and structure factors were deposited in the Protein Data Bank with the following accession codes: TtCinA apoprotein, 4CT8; NCN complex, 4UOC; ADP-ribose complex, 4UUX; ATP complex, 4CTA; AMP/Mg2+ complex, 4UUW. […]

Pipeline specifications

Software tools xia2, XDS, CCP4, PHENIX, Coot, MolProbity, PROCHECK
Applications Small-angle scattering, Protein structure analysis
Organisms Thermus thermophilus
Chemicals Adenosine Diphosphate, Adenosine Monophosphate, Adenosine Triphosphate, Niacinamide, Nicotinamide Mononucleotide, Ribose