3ZYT | pdb_00003zyt

Structure Determination of EstA from Arthrobacter nitroguajacolicus Rue61a

• PDB DOI: https://doi.org/10.2210/pdb3ZYT/pdb

• Classification: HYDROLASE
• Organism(s): Paenarthrobacter nitroguajacolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-25 Released: 2012-09-19 
• Deposition Author(s): Wagner, U.G., Fetzner, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal Structure Analysis of Esta from Arthrobacter Sp. Rue61A--an Insight Into Catalytic Promiscuity.

Wagner, U.G., Dimaio, F., Kolkenbrock, S., Fetzner, S.

(2014) FEBS Lett 588: 1154

• PubMed: 24613918 
• DOI: https://doi.org/10.1016/j.febslet.2014.02.045
• Primary Citation Related Structures: 
  3ZYT


• PubMed Abstract: 
  

  In this article we analyze the reasons for catalytic promiscuity of a type VIII esterase with β-lactamase fold and the ability to cleave β-lactams. We compared the structure of this enzyme to those of an esterase of the same type without any lactamase ability, an esterase with moderate lactamase ability, and a class C β-lactamase with similar fold. Our results show that for these enzymes, the difference in the substrate specificity is sterically driven.

---

Organizational Affiliation: 
• Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria. Electronic address: [e-mail].
Biochemistry Department, University of Washington, Box 357350, Seattle, WA 98195, USA.
Institute of Molecular Microbiology und Biotechnology, University of Münster, D-48149, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 40.31 kDa 
• Atom Count: 3,011 
• Modeled Residue Count: 372 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTERASE A	A	372	Paenarthrobacter nitroguajacolicus	Mutation(s): 0
UniProt
Find proteins for K4DIE4 (Paenarthrobacter nitroguajacolicus) Explore K4DIE4  Go to UniProtKB:  K4DIE4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EMC	B [auth A], C [auth A], D [auth A]	ETHYL MERCURY ION C2 H5 Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.246	α = 90
b = 191.246	β = 90
c = 191.246	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHENIX-ROSETTA	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Wagner, U.G., Fetzner, S.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other