Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Crystal structures of Gbetagamma and PLCbeta3 (PDB IDs 1GP2 and 4GNK) were rigid-body fit into the cryo-EM map using Chimera (58). The model was then ...
Crystal structures of Gbetagamma and PLCbeta3 (PDB IDs 1GP2 and 4GNK) were rigid-body fit into the cryo-EM map using Chimera (58). The model was then refined using molecular dynamic flexible fitting (MDFF)(48). MDFF configuration files were generated using VMD. During MDFF simulation, Gbetagamma was set as rigid with domain restraints. The MDFF simulation was conducted with a grid scaling value of 0.5 for 100 ps, followed by 3,000 steps of energy minimization until convergence of the protein RMSD. The MDFF generated model was inspected and manually adjusted in Coot, guided through the use of deep-learning-based amino-acid-wise model quality (DAQ) scoring, and refined in PHENIX.