3KC2 | pdb_00003kc2

Crystal structure of mitochondrial HAD-like phosphatase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3KC2/pdb

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


• Deposited: 2009-10-20 Released: 2009-11-24 
• Deposition Author(s): Nocek, B., Evdokimova, E., Kuznetsova, K., Iakunine, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.169 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Literature

Crystal structure of mitochondrial HAD-like phosphatase from Saccharomyces cerevisiae

Nocek, B., Evdokimova, E., Kuznetsova, K., Iakunine, A., Savchenko, A., Edwards, A., Joachimiak, A.

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)

Macromolecule Content

• Total Structure Weight: 79.74 kDa 
• Atom Count: 6,029 
• Modelled Residue Count: 646 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YKR070W	A, B	352	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: YKR070W EC: 3
UniProt
Find proteins for P36151 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36151  Go to UniProtKB:  P36151

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	E [auth A], F [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 1.55 Å
• R-Value Free:  0.169 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.734	α = 90
b = 67.095	β = 110.45
c = 76.899	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Nocek, B., Evdokimova, E., Kuznetsova, K., Iakunine, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary