37LX | pdb_000037lx

Crystal structure of apo KomA from the bacterial Kongming phage-defense system

• PDB DOI: https://doi.org/10.2210/pdb37LX/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2026-07-25 Released: 2026-11-11 
• Deposition Author(s): Zhou, J., Horton, J.R., Cheng, X.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Cancer Prevention and Research Institute of Texas (CPRIT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.258 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of apo KomA from the bacterial Kongming phage-defense system

Zhou, J., Horton, J.R., Cheng, X.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 37.12 kDa 
• Atom Count: 2,378 
• Modeled Residue Count: 301 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KomA	A	328	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.258 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.537	α = 90
b = 46.537	β = 90
c = 243.437	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-11 
Deposition Author(s): Zhou, J., Horton, J.R., Cheng, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35GM134744
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR160029

Revision History  

• Version 1.0: 2026-11-11
  Type: Initial release