3MIL | pdb_00003mil

Crystal structure of isoamyl acetate-hydrolyzing esterase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3MIL/pdb

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


• Deposited: 2010-04-11 Released: 2010-11-24 
• Deposition Author(s): Ma, J., Lu, Q., Yuan, Y., Li, K., Ge, H., Go, Y., Niu, L., Teng, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.218 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of isoamyl acetate-hydrolyzing esterase from Saccharomyces cerevisiae reveals a novel active site architecture and the basis of substrate specificity

Ma, J., Lu, Q., Yuan, Y., Ge, H., Li, K., Zhao, W., Gao, Y., Niu, L., Teng, M.

(2011) Proteins 79: 662-668

• PubMed: 21069734 
• DOI: https://doi.org/10.1002/prot.22865
• Primary Citation Related Structures: 
  3MIL

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Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.

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: 55.43 kDa 
• Atom Count: 4,591 
• Modeled Residue Count: 478 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoamyl acetate-hydrolyzing esterase	A, B	240	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: EST2, IAH1, O3287, YOR126C, YOR3287C EC: 3.1 (PDB Primary Data), 3.1.1.112 (UniProt)
UniProt
Find proteins for P41734 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41734  Go to UniProtKB:  P41734

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.218 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.565	α = 90
b = 44.644	β = 114.44
c = 81.842	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-24 
Deposition Author(s): Ma, J., Lu, Q., Yuan, Y., Li, K., Ge, H., Go, Y., Niu, L., Teng, M.

Revision History  

• Version 1.0: 2010-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-19
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations