5BUX | pdb_00005bux

Crystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Yersinia pestis with glycerol bound

• PDB DOI: https://doi.org/10.2210/pdb5BUX/pdb

• Classification: LYASE
• Organism(s): Yersinia pestis KIM10+
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-04 Released: 2016-06-08 
• Deposition Author(s): McGillick, B., Kumaran, D., Swaminathan, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Yersinia pestis with glycerol bound

McGillick, B., Kumaran, D., Swaminathan, S.

To be published.

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: 43.01 kDa 
• Atom Count: 2,503 
• Modeled Residue Count: 285 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ	A, B	191	Yersinia pestis KIM10+	Mutation(s): 0  Gene Names: fabZ, YPA_0531 EC: 4.2.1.59
UniProt
Find proteins for Q1CAM3 (Yersinia pestis bv. Antiqua (strain Antiqua)) Explore Q1CAM3  Go to UniProtKB:  Q1CAM3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN	E [auth A], F [auth B], G [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.76	α = 90
b = 104.76	β = 90
c = 87.961	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): McGillick, B., Kumaran, D., Swaminathan, S.

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description