4ZR8 | pdb_00004zr8

Structure of uroporphyrinogen decarboxylase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb4ZR8/pdb

• Classification: LYASE
• Organism(s): Acinetobacter baumannii AB5075
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-11 Released: 2015-06-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Literature

Structure of uroporphyrinogen decarboxylase from Acinetobacter baumannii

Abendroth, J., Fairman, J.W., 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: 81.43 kDa 
• Atom Count: 6,397 
• Modeled Residue Count: 707 
• Deposited Residue Count: 730 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen decarboxylase	A, B	365	Acinetobacter baumannii AB5075	Mutation(s): 0  Gene Names: hemE, A591_A1129 EC: 4.1.1.37
UniProt
Find proteins for A0A0M3KL37 (Acinetobacter baumannii AB5075) Explore A0A0M3KL37  Go to UniProtKB:  A0A0M3KL37

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34ZR8

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.54	α = 90
b = 83.38	β = 106.97
c = 68.46	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations