9QRN | pdb_00009qrn

DNA polymerase without DNA or inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9QRN/pdb
• EM Map EMD-53320: EMDB EMDataResource
• NAKB: 9QRN

• Classification: DNA BINDING PROTEIN
• Organism(s): Enterococcus faecium, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-04-03 Released: 2025-09-24 
• Deposition Author(s): Lamers, M.H., Urem, M., Smits, W.K.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

DNA polymerase without DNA or inhibitor

Lamers, M.H., Urem, M., Smits, W.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 167.79 kDa 
• Atom Count: 8,842 
• Modeled Residue Count: 1,116 
• Deposited Residue Count: 1,477 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III PolC-type	A	1,474	Enterococcus faecium	Mutation(s): 2  Gene Names: polC, M3X98_02600 EC: 2.7.7.7
UniProt
Find proteins for A0A9X4B319 (Enterococcus faecium) Explore A0A9X4B319  Go to UniProtKB:  A0A9X4B319

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*A)-3')	B [auth E]	3	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Lamers, M.H., Urem, M., Smits, W.K.

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Funding Organization	Location	Grant Number
Other government	Netherlands	POLSTOP2

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release