4R8O

Crystal structure of a DUF3836 family protein (BVU_1206) from Bacteroides vulgatus ATCC 8482 at 2.50 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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: 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 t ...

    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

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinAB104Bacteroides vulgatus ATCC 8482Mutation(s): 0 
Gene Names: BVU_1206
Find proteins for A6KZN2 (Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / NBRC 14291 / NCTC 11154))
Explore A6KZN2 
Go to UniProtKB:  A6KZN2
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.08α = 90
b = 98.08β = 90
c = 89.24γ = 120
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Structure summary
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2020-04-22
    Changes: Database references, Derived calculations