4WSH

Crystal structure of Probable Uroporphyrinogen decarboxylase (UPD) (URO-D) from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb4WSH/pdb

• Classification: LYASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-27 Released: 2014-11-19 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.201 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 

Literature

Crystal structure of Probable Uroporphyrinogen decarboxylase (UPD) (URO-D) from Pseudomonas aeruginosa

Abendroth, J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

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)

Macromolecule Content

• Total Structure Weight: 80.67 kDa 
• Atom Count: 5,849 
• Modelled Residue Count: 702 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen decarboxylase	A, B	363	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: hemE, PA5034 EC: 4.1.1.37
UniProt
Find proteins for P95458 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P95458  Go to UniProtKB:  P95458

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.201 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M34WSH

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.76	α = 90
b = 73.88	β = 90
c = 141.88	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references