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.
Cryo-EM structure of the AlbAB cyclodipeptide oxidase enzyme filament
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
AlbAB cyclodipeptide oxidase enzyme filament
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Grid was plunge frozen into liquid ethane using the following parameters:
blot force- 5, blot time 2 seconds
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
795765
Reported Resolution (Å)
2.78
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Final reconstruction was generated by a masked local refinement of the helically refined map. The mask encompassed one dimer of AlbA and two surroundi ...
Final reconstruction was generated by a masked local refinement of the helically refined map. The mask encompassed one dimer of AlbA and two surrounding dimers of AlbB.
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C1
Axial Rise
46.063
Angular Rotation
119.969
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Cross-correlation coefficient
Overall B Value
107.4
Fitting Procedure
Details
A model of AlbAB was created using AlphaFold2 using MMseqs2 via ColabFold. The model was then fit into the cryoEM density using ChimeraX. The model wa ...
A model of AlbAB was created using AlphaFold2 using MMseqs2 via ColabFold. The model was then fit into the cryoEM density using ChimeraX. The model was then iteratively refined using Coot v 0.9.8.1 and real-space refinement in Phenix v 1.20.1-4487.