6FWY | pdb_00006fwy

Thioester domain of the Enterococcus faecium TIE86 protein

• PDB DOI: https://doi.org/10.2210/pdb6FWY/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-07 Released: 2018-08-08 
• Deposition Author(s): Miller, O.K., Banfield, M.J., Schwarz-Linek, U.
• Funding Organization(s): Medical Research Council (United Kingdom), Royal Society of Edinburgh

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

A new structural class of bacterial thioester domains reveals a slipknot topology.

Miller, O.K., Banfield, M.J., Schwarz-Linek, U.

(2018) Protein Sci 27: 1651-1660

• PubMed: 30052296 
• DOI: https://doi.org/10.1002/pro.3478
• Primary Citation Related Structures: 
  6FWV, 6FWY, 6FX6


• PubMed Abstract: 
  

  An increasing number of surface-associated proteins identified in Gram-positive bacteria are characterized by intramolecular cross-links in structurally conserved thioester, isopeptide, and ester domains (TIE proteins). Two classes of thioester domains (TEDs) have been predicted based on sequence with, to date, only representatives of Class I structurally characterized. Here, we present crystal structures of three Class II TEDs from Bacillus anthracis, vancomycin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococcus faecium. These proteins are structurally distinct from Class I TEDs due to a β-sandwich domain that is inserted into the conserved TED fold to form a slipknot structure. Further, the B. anthracis TED domain is presented in the context of a full-length sortase-anchored protein structure (BaTIE). This provides insight into the three-dimensional arrangement of TIE proteins, which emerge as very abundant putative adhesins of Gram-positive bacteria.

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Organizational Affiliation: 
• Biomedical Sciences Research Complex and School of Biology, University of St Andrews, St Andrews, KY16 9ST, United Kingdom.
John Innes Centre, Department of Biological Chemistry, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 121.76 kDa 
• Atom Count: 8,947 
• Modeled Residue Count: 1,118 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-type Cna protein	A, B, C, D	280	Enterococcus faecium	Mutation(s): 0  Gene Names: B4W81_16995, BTA13_08335, DTPHA_1402599

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	F [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.7	α = 90
b = 33.732	β = 105.88
c = 206.052	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
SHELXD	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Miller, O.K., Banfield, M.J., Schwarz-Linek, U.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/K001485
Royal Society of Edinburgh	United Kingdom	--

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2018-10-31
  Changes: Data collection, Database references
• Version 1.2: 2019-01-23
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Refinement description