Computational protocol: A Conserved Acidic Residue in Phenylalanine HydroxylaseContributes to Cofactor Affinity and Catalysis

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Protocol publication

[…] The program molrep from the ccp4 suite was used to determine the structure using a previously published structure of apo-cPAH (PDB entry 1LTU). For molrep, all water molecules and other ions such as iron and chloride were removed from the aforementioned model to limit model bias. Several cycles of refinement and model building proceeded using Refmac5 and Coot, respectively. Anisotropic B factors were used during the refinement of all D139 mutant structures. Weights were also optimized during the refinement process. The crystallographic data and refinement statistics are listed in Table . All figures were rendered with PYMOL (version […]

Pipeline specifications

Software tools Molrep, CCP4, REFMAC5, Coot, PyMOL
Application Protein structure analysis
Organisms Chromobacterium violaceum
Chemicals Hydrogen, Iron