8EPZ

Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mn

• PDB DOI:  https://doi.org/10.2210/pdb8EPZ/pdb

• Classification: LYASE
• Organism(s): Paralcaligenes ureilyticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-07 Released: 2023-02-22 
• Deposition Author(s): Bayaraa, T., Lonhienne, T., Guddat, L.W.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg

Bayaraa, T., Lonhienne, T., Guddat, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
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: 125.96 kDa 
• Atom Count: 8,706 
• Modelled Residue Count: 1,137 
• Deposited Residue Count: 1,150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroxyacid dehydratase	A, B	575	Paralcaligenes ureilyticus	Mutation(s): 0  Gene Names: EDC26_11947
UniProt
Find proteins for A0A4R3LQ44 (Paralcaligenes ureilyticus) Explore A0A4R3LQ44  Go to UniProtKB:  A0A4R3LQ44

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES (Subject of Investigation/LOI)	C [auth A], H [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)	G [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
MN (Subject of Investigation/LOI)	D [auth A], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CO2 (Subject of Investigation/LOI)	E [auth A], F [auth A], J [auth B]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.639	α = 90
b = 113.135	β = 90
c = 182.891	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Bayaraa, T., Lonhienne, T., Guddat, L.W.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP210101802

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release