wwPDB validation report of PDB entry 5OG1

Initial models of the BAPDWB monomer were generated using MODELLER v9.17 with previously determined crystal structures of ClpB or ClpB domains as templates (PDB ids 4CIU, 1QVR, 4HSE and 4LJ9). The crystal structure of E. coli ClpB (4CIU) was used as a main template, the crystal structure of T. thermophilus (1QVR) was used to model positions of the NTD and the crystal structures of AAA1 and AAA2 of E. coli ClpB (4HSE and 4LJ9) were used to model the pore loops disordered in other crystal structures. Initial rigid body fitting of the monomers in the map was manually done in Chimera using the Fit-in-Map tool. iMODFIT was used for fitting involving large domain motions. FlexEM was then used for refinement of secondary structures and loops in the map. Quality and improvement of the fit was assessed with TEMPy using the Segment based Manders Overlap Coefficient (SMOC) scores and segment based cross correlation scores. Rigid body fitting of ATPgammaS (structure extracted from PDB id 3EIH) into the nucleotide binding sites was manually done in Chimera using the Fit-in-Map tool. The target map for fitting of ATPgammaS was the difference map between experimental map and map generated using the nucleotide-free model reveiling nucleotide densities. A round of real-space refinement was performed in phenix using energy minimization to fix the model's geometry and clashes.

ClpB (BAP form, double walker B mutant) homohexamer in the ATPgammaS state

Chaperone protein ClpB,ATP-dependent Clp protease ATP-binding subunit ClpA,Chaperone protein ClpB

PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

Heat shock protein F84.1,Heat shock protein F84.1

ClpB (BAP form, double walker B mutant) in the ATPgammaS state

ClpB (BAP form, double walker B mutant) in the ATPgammaS state bound to the model substrate casein

Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state
Calculated fsc threesigma indicator curve
Author provided fsc threesigma indicator curve
Author provided fsc halfbit indicator curve
Author provided fsc onebit indicator curve
Author provided fsc 0.333 indicator curve
Author provided fsc 0.143 indicator curve
geometric validation package for ligand chemistry in protein x-ray structures
20191225.v01 (using entries in the PDB archive December 25th 2019)