3D6X | pdb_00003d6x

Crystal structure of Campylobacter jejuni FabZ

• PDB DOI: https://doi.org/10.2210/pdb3D6X/pdb

• Classification: LYASE
• Organism(s): Campylobacter jejuni subsp. jejuni 81-176
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-20 Released: 2009-05-05 
• Deposition Author(s): Yokoyama, T., Yeo, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Campylobacter jejuni fatty acid synthase II: structural and functional analysis of beta-hydroxyacyl-ACP dehydratase (FabZ).

Kirkpatrick, A.S., Yokoyama, T., Choi, K.J., Yeo, H.J.

(2009) Biochem Biophys Res Commun 380: 407-412

• PubMed: 19280690 
• DOI: https://doi.org/10.1016/j.bbrc.2009.01.115
• Primary Citation of Related Structures:  
  3D6X


• PubMed Abstract: 
  

  Fatty acid biosynthesis is crucial for all living cells. In contrast to higher organisms, bacteria use a type II fatty acid synthase (FAS II) composed of a series of individual proteins, making FAS II enzymes excellent targets for antibiotics discovery. The beta-hydroxyacyl-ACP dehydratase (FabZ) catalyzes an essential step in the FAS II pathway. Here, we report the structure of Campylobacter jejuni FabZ (CjFabZ), showing a hexamer both in crystals and solution, with each protomer adopting the characteristic hot dog fold. Together with biochemical analysis of CjFabZ, we define the first functional FAS II enzyme from this pathogen, and provide a framework for investigation on roles of FAS II in C. jejuni virulence.

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Organizational Affiliation: 

Department of Biology and Biochemistry, University of Houston, 4800 Calhoun, Houston, TX 77204, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 101.02 kDa 
• Atom Count: 6,635 
• Modelled Residue Count: 837 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase	A, B, C, D, E, F	146	Campylobacter jejuni subsp. jejuni 81-176	Mutation(s): 0  Gene Names: fabZ, CJJ81176_0300 EC: 4.2.1 (PDB Primary Data), 4.2.1.59 (UniProt)
UniProt
Find proteins for A1VXZ7 (Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176)) Explore A1VXZ7  Go to UniProtKB:  A1VXZ7

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.589	α = 90
b = 93.403	β = 90
c = 126.631	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Yokoyama, T., Yeo, H.J.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary