8I3N

crystal structure of yeast cytosine deaminase mutant yCD-RQ

• PDB DOI: https://doi.org/10.2210/pdb8I3N/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-17 Released: 2024-01-24 
• Deposition Author(s): Qin, M.M., Yao, L.S., Deng, H.Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.218 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Literature

The crystal structure of rational designed yCD mutant yCD-RQ

Qin, M.M., Yao, L.S.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.19 kDa 
• Atom Count: 5,134 
• Modelled Residue Count: 608 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine deaminase	A, B, C, D	177	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: FCY1 EC: 3.5.4.1
UniProt
Find proteins for Q12178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12178  Go to UniProtKB:  Q12178

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.218 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.669	α = 90
b = 64.47	β = 97.97
c = 83.092	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
XDS	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Qin, M.M., Yao, L.S., Deng, H.Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32201011

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release