6FX6 | pdb_00006fx6

Thioester domain of the Staphylococcus aureus TIE protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.246 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6FX6

This is version 2.1 of the entry. See complete history. 

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

  • 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.

    • Organizational Affiliation: 
    • Biomedical Sciences Research Complex and School of Biology, University of St Andrews, St Andrews, KY16 9ST, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 28.73 kDa 
  • Atom Count: 1,953 
  • Modeled Residue Count: 237 
  • Deposited Residue Count: 253 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SaTIE-TED253Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A3F2YM24 (Staphylococcus aureus)
Explore A0A3F2YM24 
Go to UniProtKB:  A0A3F2YM24
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3F2YM24
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.029α = 90
b = 73.612β = 90
c = 74.651γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
SHELXDphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/K001485
Royal Society of EdinburghUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary