2O3K | pdb_00002o3k

Yeast Cytosine Deaminase D92E Triple Mutant bound to transition state analogue HPY

• PDB DOI: https://doi.org/10.2210/pdb2O3K/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-01 Released: 2007-10-16 
• Deposition Author(s): Korkegian, A.M., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Yeast Cytosine Deaminase D92E Triple Mutant bound to transition state analogue HPY

Stolworthy, T., Korkegian, A.M., Willmon, C., Stoddard, B.L., Black, M.E.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 36.06 kDa 
• Atom Count: 2,548 
• Modeled Residue Count: 307 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine deaminase	A, B	161	Saccharomyces cerevisiae	Mutation(s): 4  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
HPY	D [auth A], G [auth B]	4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE C4 H6 N2 O2 DEAAWXYGBWCVJW-VKHMYHEASA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.257 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.916	α = 90
b = 69.09	β = 90
c = 74.174	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Korkegian, A.M., Stoddard, B.L.

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description