9X8G | pdb_00009x8g

Crystal structure of Campylobacter jejuni DapE

• PDB DOI: https://doi.org/10.2210/pdb9X8G/pdb

• Classification: HYDROLASE
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-19 Released: 2026-10-28 
• Deposition Author(s): Ahn, S.Y., You, Y.B., Yoon, S.I.
• Funding Organization(s): National Research Foundation (NRF, Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: in silico

Literature

Structural analysis of the putative succinyl-diaminopimelic acid desuccinylase DapE from Campylobacter jejuni

Yoon, S.I.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 82.51 kDa 
• Atom Count: 5,565 
• Modeled Residue Count: 693 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-diaminopimelate desuccinylase	A, B	371	Campylobacter jejuni	Mutation(s): 0  Gene Names: dapE, Cj1048c EC: 3.5.1.18
UniProt
Find proteins for Q0P9K4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P9K4  Go to UniProtKB:  Q0P9K4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.678	α = 90
b = 116.712	β = 90
c = 198.961	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Ahn, S.Y., You, Y.B., Yoon, S.I.

---

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2023-00208153

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release