5EO6 | pdb_00005eo6

Coproporphyrinogen III oxidase (HemF) from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb5EO6/pdb

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


• Deposited: 2015-11-10 Released: 2015-12-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.168 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Structure of oproporphyrinogen III oxidase (aerobic) from Acinetobacter baumannii

Abendroth, J., Mayclin, S.J., 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: 74.98 kDa 
• Atom Count: 5,862 
• Modeled Residue Count: 619 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproporphyrinogen oxidase	A, B	324	Acinetobacter baumannii	Mutation(s): 0  Gene Names: hemF, ABUW_0377, ACX61_01995, AKG96_15100 EC: 1.3.3.3
UniProt
Find proteins for A0A0D5YE19 (Acinetobacter baumannii) Explore A0A0D5YE19  Go to UniProtKB:  A0A0D5YE19

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.168 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35EO6

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.14	α = 90
b = 97.16	β = 115.79
c = 71.26	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description