3F4A | pdb_00003f4a

Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family

• PDB DOI: https://doi.org/10.2210/pdb3F4A/pdb

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


• Deposited: 2008-10-31 Released: 2008-11-25 
• Deposition Author(s): Singer, A.U., Xu, X., Cui, H., Osipiuk, J., Joachimiak, A., Edwards, A.M., Yakunin, A.F., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.211 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family

Proudfoot, M., Brown, G., Singer, A.U., Xu, X., Cui, H., Edwards, A.M., Joachimiak, A., Savchenko, A., Yakunin, A.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.8 kDa 
• Atom Count: 2,816 
• Modeled Residue Count: 288 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YGR203W	A, B	169	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: G7731, YGR203W EC: 3.1.3.16 (PDB Primary Data), 3.1.3 (UniProt)
UniProt
Find proteins for P42937 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P42937  Go to UniProtKB:  P42937

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NH4	L [auth B]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.211 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.382	α = 90
b = 72.025	β = 103.6
c = 53.514	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Singer, A.U., Xu, X., Cui, H., Osipiuk, J., Joachimiak, A., Edwards, A.M., Yakunin, A.F., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary