4EWT

The crystal structure of a putative aminohydrolase from methicillin resistant Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb4EWT/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-27 Released: 2013-02-20 
• Deposition Author(s): Girish, T.S., Vivek, B., Colaco, M., Misquith, S., Gopal, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Structure of an amidohydrolase, SACOL0085, from methicillin-resistant Staphylococcus aureus COL

Girish, T.S., Vivek, B., Colaco, M., Misquith, S., Gopal, B.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 103-108

• PubMed: 23385746 
• DOI: https://doi.org/10.1107/S1744309112049822
• Primary Citation of Related Structures:  
  4EWT


• PubMed Abstract: 
  

  Staphylococcus aureus is an opportunistic pathogen that rapidly acquires resistance to frontline antibiotics. The characterization of novel protein targets from this bacterium is thus an important step towards future therapeutic strategies. Here, the crystal structure of an amidohydrolase, SACOL0085, from S. aureus COL is described. SACOL0085 is a member of the M20D family of peptidases. Unlike other M20D peptidases, which are either monomers or dimers, SACOL0085 adopts a butterfly-shaped homotetrameric arrangement with extensive intersubunit interactions. Each subunit of SACOL0085 contains two Mn(2+) ions at the active site. A conserved cysteine residue at the active site distinguishes M20D peptidases from other M20 family members. This cysteine, Cys103, serves as bidentate ligand coordinating both Mn(2+) ions in SACOL0085.

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Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 174.18 kDa 
• Atom Count: 12,344 
• Modelled Residue Count: 1,542 
• Deposited Residue Count: 1,568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase, M20/M25/M40 family	A, B [auth C], C [auth D], D [auth B]	392	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: SACOL0085 EC: 3.5.1.14
UniProt
Find proteins for A0A0H2WZV8 (Staphylococcus aureus (strain COL)) Explore A0A0H2WZV8  Go to UniProtKB:  A0A0H2WZV8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE7	L [auth D], O [auth B], P [auth B]	1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL C14 H30 O7 S ACMBXVJDKVNCGH-UHFFFAOYSA-N
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN	E [auth A], F [auth A], H [auth C], I [auth C], J [auth D], K [auth D], M [auth B], N [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.62	α = 115.4
b = 120.11	β = 94.64
c = 132.41	γ = 96.55

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Girish, T.S., Vivek, B., Colaco, M., Misquith, S., Gopal, B.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description