3E2V | pdb_00003e2v

Crystal structure of an uncharacterized amidohydrolase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3E2V/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae YJM789
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-06 Released: 2008-08-26 
• Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of an uncharacterized amidohydrolase from Saccharomyces cerevisiae

Bonanno, J.B., Dickey, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.3 kDa 
• Atom Count: 6,568 
• Modeled Residue Count: 725 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3'-5'-exonuclease	A, B	401	Saccharomyces cerevisiae YJM789	Mutation(s): 0  Gene Names: SCY_0164
UniProt
Find proteins for A6ZKP4 (Saccharomyces cerevisiae (strain YJM789)) Explore A6ZKP4  Go to UniProtKB:  A6ZKP4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], F [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth A], G [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.532	α = 90
b = 55.007	β = 95.85
c = 115.26	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary