7UFT | pdb_00007uft

Cryo-EM Structure of Bl_Man38C at 2.9 A

• PDB DOI: https://doi.org/10.2210/pdb7UFT/pdb
• EM Map EMD-26480: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Bifidobacterium longum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-23 Released: 2022-11-16 
• Deposition Author(s): Santos, C.R., Cordeiro, R.L., Domingues, M.N., Borges, A.C., de Farias, M.A., Van Heel, M., Murakami, M.T., Portugal, R.V.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structure of Bl_Man38C at 2.9 A

Santos, C.R., Cordeiro, R.L., Domingues, M.N., Borges, A.C., de Farias, M.A., Van Heel, M., Murakami, M.T., Portugal, R.V.

(2022) Nat Chem Biol 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 470.87 kDa 
• Atom Count: 32,324 
• Modeled Residue Count: 4,128 
• Deposited Residue Count: 4,228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-mannosidase	A, B, C, D	1,057	Bifidobacterium longum	Mutation(s): 0  Gene Names: BL1329
UniProt
Find proteins for Q8G4P9 (Bifidobacterium longum (strain NCC 2705)) Explore Q8G4P9  Go to UniProtKB:  Q8G4P9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cisTEM

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Santos, C.R., Cordeiro, R.L., Domingues, M.N., Borges, A.C., de Farias, M.A., Van Heel, M., Murakami, M.T., Portugal, R.V.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/26982-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2017/15340-2

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-06-12
  Changes: Data collection