8HNU | pdb_00008hnu

Cellodextrin phosphorylase stable variant from Clostridium thermocellum

• PDB DOI: https://doi.org/10.2210/pdb8HNU/pdb
• EM Map EMD-34918: EMDB EMDataResource

• Classification: CARBOHYDRATE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-12-08 Released: 2023-12-13 
• Deposition Author(s): Kuga, T., Sunagawa, N., Igarashi, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

11 cysteine-to-serine mutations improve the stability of cellodextrin phosphorylase

Kuga, T., Sunagawa, N., Igarashi, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 225.61 kDa 
• Atom Count: 16,178 
• Modeled Residue Count: 1,970 
• Deposited Residue Count: 1,986 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellodextrin phosphorylase	A, B	993	Acetivibrio thermocellus	Mutation(s): 12  Gene Names: cdp-ym4
UniProt
Find proteins for Q93HT8 (Acetivibrio thermocellus) Explore Q93HT8  Go to UniProtKB:  Q93HT8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.0
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Kuga, T., Sunagawa, N., Igarashi, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22J12566

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release