8I3P | pdb_00008i3p

crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one

• PDB DOI: https://doi.org/10.2210/pdb8I3P/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.161 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one

Qin, M.M., Deng, H.Z., 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

Macromolecule Content 

• Total Structure Weight: 46.01 kDa 
• Atom Count: 2,885 
• Modeled Residue Count: 330 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine deaminase	A, B	198	Saccharomyces cerevisiae S288C	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OS0 (Subject of Investigation/LOI)	C [auth A], F [auth B]	4-oxidanyl-3,4-dihydro-1H-pyrimidin-2-one C4 H6 N2 O2 DEAAWXYGBWCVJW-UHFFFAOYSA-N
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.161 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.175	α = 90
b = 68.9	β = 101.58
c = 49.424	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
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., Deng, H.Z., Yao, L.S.

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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