8HZ1 | pdb_00008hz1

Ambient temperature crystal structure of Escherichia coli CyaY

• PDB DOI: https://doi.org/10.2210/pdb8HZ1/pdb

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


• Deposited: 2023-01-07 Released: 2023-01-25 
• Deposition Author(s): Shafiei, A., DeMirci, H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.356 (Depositor), 0.356 (DCC) 
• R-Value Work: 
  0.316 (Depositor), 0.316 (DCC) 
• R-Value Observed: 
  0.320 (Depositor) 

Starting Model: experimental

Literature

Comparative Structural Analysis of Escherichia Coli Cyay at Room and Cryogenic Temperatures Using Macromolecular and Serial Crystallography.

Shafiei, A., Baldir, N., Na, J., Kim, J.H., DeMirci, H.

(2025) Chembiochem 26: e202500442-e202500442

• PubMed: 41147201 
• DOI: https://doi.org/10.1002/cbic.202500442


• PubMed Abstract: 
  

  Frataxin is a 23 kDa mitochondrial iron-binding protein involved in the biogenesis of iron-sulfur (Fe-S) clusters. Deficiency in frataxin is associated with Friedreich's ataxia, a progressive neurodegenerative disorder. CyaY, the bacterial ortholog of eukaryotic frataxin, is believed to function as an iron donor in Fe-S cluster assembly, making it a key target for structural and functional studies. In this work, a comprehensive structural analysis of the Escherichia coli CyaY protein is presented, comparing its structure at room temperature and cryogenic conditions. Notably, the first room-temperature structures are obtained using the Turkish Light Source "Turkish DeLight" X-ray diffractometer and serial synchrotron X-ray crystallography, marking a significant step forward in understanding CyaY under near-physiological conditions.

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Organizational Affiliation: 
• Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey.
Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea.
SLAC National Laboratory, Stanford PULSE Institute, Menlo Park, 94025, CA, USA.
Koc University Isbank Center for Infectious Diseases (KUISCID), Koc University, 34010, Istanbul, Turkey.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 12.24 kDa 
• Atom Count: 906 
• Modeled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur cluster assembly protein CyaY	A	106	Escherichia coli	Mutation(s): 0  Gene Names: cyaY
UniProt
Find proteins for P27838 (Escherichia coli (strain K12)) Explore P27838  Go to UniProtKB:  P27838

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.356 (Depositor), 0.356 (DCC) 
• R-Value Work:  0.316 (Depositor), 0.316 (DCC) 
• R-Value Observed: 0.320 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.167	α = 90
b = 45.167	β = 90
c = 101.129	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Shafiei, A., DeMirci, H.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2026-05-06
  Changes: Database references, Structure summary