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.
CryoEM structure of Toxin B (TcdB) from clostridioides difficile complexed with methyl cholate
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
P18177
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
12.9779
f_angle_d
0.5023
f_chiral_restr
0.0429
f_plane_restr
0.0038
f_bond_d
0.0032
Sample
Clostridioides difficile Toxin B (TcdB) complexed with the synthetic bile acid methyl cholate
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
30s preblot incubation on grid.
2-3s blot time.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
339310
Reported Resolution (Å)
2.87
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Predicted models were docked into the map using ChimeraX. The model was then manually built with ISOLDE and Coot and refined with
phenix.real_space_r ...
Predicted models were docked into the map using ChimeraX. The model was then manually built with ISOLDE and Coot and refined with
phenix.real_space_refine.