3NUQ | pdb_00003nuq

Structure of a putative nucleotide phosphatase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3NUQ/pdb

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


• Deposited: 2010-07-07 Released: 2010-08-18 
• Deposition Author(s): Dong, A., Yang, C., Singer, A.U., Evdokimova, E., Kudritsdka, M., Brown, G., Edwards, A.M., Joachimiak, A., Savchenko, A., Yakunin, A.F., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structure of a putative nucleotide phosphatase from Saccharomyces cerevisiae

Brown, G., Evdokimova, E., Kudritska, M., Dong, A., Yang, C., Singer, A.U., Edwards, A.M., Savchenko, A., Yakunin, A.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.53 kDa 
• Atom Count: 2,380 
• Modeled Residue Count: 268 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative nucleotide phosphatase	A	282	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SDT1, SSM1, YGL224C EC: 3.1.3.5
UniProt
Find proteins for P53078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53078  Go to UniProtKB:  P53078

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.474	α = 90
b = 64.664	β = 90
c = 67.708	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
SHELXCD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Dong, A., Yang, C., Singer, A.U., Evdokimova, E., Kudritsdka, M., Brown, G., Edwards, A.M., Joachimiak, A., Savchenko, A., Yakunin, A.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description