6W2O

Crystal structure of uroporphyrinogen III decarboxylate (hemE) from Stenotrophomonas maltophilia

• PDB DOI: https://doi.org/10.2210/pdb6W2O/pdb

• Classification: LYASE
• Organism(s): Stenotrophomonas maltophilia K279a
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-06 Released: 2020-04-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.171 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

Crystal structure of uroporphyrinogen III decarboxylate (hemE) from Stenotrophomonas maltophilia

Edwards, T.E., Davies, D.R., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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: gel filtration

Macromolecule Content

• Total Structure Weight: 40.61 kDa 
• Atom Count: 3,247 
• Modelled Residue Count: 355 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen decarboxylase	A	365	Stenotrophomonas maltophilia K279a	Mutation(s): 0  Gene Names: hemE, Smlt3622 EC: 4.1.1.37
UniProt
Find proteins for B2FQJ0 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FQJ0  Go to UniProtKB:  B2FQJ0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.171 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.69	α = 90
b = 103.69	β = 90
c = 74.72	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description