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)

Experimental Data Snapshot

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

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9UZ6

This is version 1.0 of the entry. See complete history.

Literature

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

Han, Z., Zeng, A.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33195
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.