3OPX

Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb3OPX/pdb

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


• Deposited: 2010-09-02 Released: 2011-03-02 
• Deposition Author(s): Teng, M.K., Niu, L.W., Shi, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.251 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate

Shi, N., Teng, M.K., Niu, L.W.

To be published.

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: 30.54 kDa 
• Atom Count: 2,175 
• Modelled Residue Count: 247 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SSM1	A	263	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: SSM1, SDT1, YGL224C
UniProt
Find proteins for P53078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53078  Go to UniProtKB:  P53078

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	C [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.251 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.198	α = 90
b = 78.037	β = 90
c = 82.789	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-02 
Deposition Author(s): Teng, M.K., Niu, L.W., Shi, N.

Revision History  

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description