9UZ6 | pdb_00009uz6

Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo

• PDB DOI: https://doi.org/10.2210/pdb9UZ6/pdb
• EM Map EMD-64637: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli str. K-12 substr. DH10B
• Expression System: Cloning vector pET-28a-ZaTdT12
• Mutation(s): No 


• Deposited: 2025-05-16 Released: 2025-12-31 
• Deposition Author(s): Han, Z., Zeng, A.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo

Han, Z., Zeng, A.

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: 211.23 kDa 
• Atom Count: 14,192 
• Modeled Residue Count: 1,866 
• Deposited Residue Count: 1,932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine dehydrogenase (decarboxylating)	A, B	966	Escherichia coli str. K-12 substr. DH10B	Mutation(s): 0  Gene Names: gcvP, b2903, JW2871 EC: 1.4.4.2
UniProt
Find proteins for P33195 (Escherichia coli (strain K12)) Explore P33195  Go to UniProtKB:  P33195

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Han, Z., Zeng, A.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release