8PHL

Human carbonic anhydrase II containing 4-fluorophenylalanine

• PDB DOI: https://doi.org/10.2210/pdb8PHL/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-20 Released: 2024-03-06 
• Deposition Author(s): Pham, L.B.T., Costantino, A., Barbieri, L., Calderone, V., Luchinat, E., Banci, L.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.194 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Controlling the incorporation of fluorinated amino acids in human cells and its structural impact.

Costantino, A., Pham, L.B.T., Barbieri, L., Calderone, V., Ben-Nissan, G., Sharon, M., Banci, L., Luchinat, E.

(2024) Protein Sci 33: e4910-e4910

• PubMed: 38358125 
• DOI: https://doi.org/10.1002/pro.4910
• Primary Citation of Related Structures:  
  8P6U, 8PHL, 8Q0C


• PubMed Abstract: 
  

  Fluorinated aromatic amino acids (FAAs) are promising tools when studying protein structure and dynamics by NMR spectroscopy. The incorporation FAAs in mammalian expression systems has been introduced only recently. Here, we investigate the effects of FAAs incorporation in proteins expressed in human cells, focusing on the probability of incorporation and its consequences on the ¹⁹ F NMR spectra. By combining ¹⁹ F NMR, direct MS and x-ray crystallography, we demonstrate that the probability of FAA incorporation is only a function of the FAA concentration in the expression medium and is a pure stochastic phenomenon. In contrast with the MS data, the x-ray structures of carbonic anhydrase II reveal that while the 3D structure is not affected, certain positions lack fluorine, suggesting that crystallization selectively excludes protein molecules featuring subtle conformational modifications. This study offers a predictive model of the FAA incorporation efficiency and provides a framework for controlling protein fluorination in mammalian expression systems.

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Organizational Affiliation: 

CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.67 kDa 
• Atom Count: 2,337 
• Modelled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	258	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBO (Subject of Investigation/LOI)	B [auth A]	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PFF	A	L-PEPTIDE LINKING	C9 H10 F N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.194 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.82	α = 90
b = 40.9	β = 104.73
c = 70.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Pham, L.B.T., Costantino, A., Barbieri, L., Calderone, V., Luchinat, E., Banci, L.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release