9F0F

Coproporphyrin III - LmCpfC WT complex soaked with Fe2+ and anomalous densities

• PDB DOI: https://doi.org/10.2210/pdb9F0F/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-04-16 Released: 2024-04-24 
• Deposition Author(s): Gabler, T., Hofauer, S.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.183 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Coproporphyrin III - LmCpfC WT complex soaked with Fe2+ and anomalous densities

Gabler, T., Hofauer, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 36.43 kDa 
• Atom Count: 2,663 
• Modelled Residue Count: 308 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproporphyrin III ferrochelatase	A	310	Listeria monocytogenes	Mutation(s): 0  Gene Names: cpfC, hemH, lmo2211 EC: 4.99.1.9
UniProt
Find proteins for Q8Y565 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y565  Go to UniProtKB:  Q8Y565

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HT9 (Subject of Investigation/LOI)	B [auth A]	coproporphyrin III C36 H38 N4 O8 XNBNKCLBGTWWSD-UJJXFSCMSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	E [auth A], F [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.183 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.158	α = 90
b = 67.73	β = 103.221
c = 62.494	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Gabler, T., Hofauer, S.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P33544

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release