4R03

Crystal structure of a DUF3836 family protein (BDI_3222) from Parabacteroides distasonis ATCC 8503 at 1.50 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of single-layer beta-sheet proteins evolved from beta-hairpin repeats.

Xu, Q.Biancalana, M.Grant, J.C.Chiu, H.J.Jaroszewski, L.Knuth, M.W.Lesley, S.A.Godzik, A.Elsliger, M.A.Deacon, A.M.Wilson, I.A.

(2019) Protein Sci 28: 1676-1689

  • DOI: https://doi.org/10.1002/pro.3683
  • Primary Citation of Related Structures:  
    3MSW, 4R03, 4R8O

  • PubMed Abstract: 

    Free-standing single-layer β-sheets are extremely rare in naturally occurring proteins, even though β-sheet motifs are ubiquitous. Here we report the crystal structures of three homologous, single-layer, anti-parallel β-sheet proteins, comprised of three or four twisted β-hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β-sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and are putatively involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent-exposed tyrosine residues, was identified on the concave surface of the β-sheet. These new modular single-layer β-sheet proteins may serve as a new model system for studying folding and design of β-rich proteins.


  • Organizational Affiliation

    Joint Center for Structural Genomics, www.jcsg.org.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein109Parabacteroides distasonis ATCC 8503Mutation(s): 0 
Gene Names: BDI_3222
UniProt
Find proteins for A6LGW3 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152))
Explore A6LGW3 
Go to UniProtKB:  A6LGW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6LGW3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.001α = 90
b = 71.697β = 90
c = 82.683γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Structure summary
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2020-04-22
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations