7FDY | pdb_00007fdy

Structure of OmpF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.295 (Depositor), 0.302 (DCC) 
  • R-Value Work: 
    0.269 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 
    0.271 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7FDY

This is version 1.2 of the entry. See complete history

Literature

Design and directed evolution of noncanonical beta-stereoselective metalloglycosidases.

Jeong, W.J.Song, W.J.

(2022) Nat Commun 13: 6844-6844

  • DOI: https://doi.org/10.1038/s41467-022-34713-8
  • Primary Citation Related Structures: 
    7FDY, 7FF7

  • PubMed Abstract: 

    Metallohydrolases are ubiquitous in nearly all subclasses of hydrolases, utilizing metal elements to activate a water molecule and facilitate its subsequent dissociation of diverse chemical bonds. However, such a catalytic role of metal ions is rarely found with glycosidases that hydrolyze the glycosidic bonds in sugars. Herein, we design metalloglycosidases by constructing a hydrolytically active Zn-binding site within a barrel-shaped outer membrane protein OmpF. Structure- and mechanism-based redesign and directed evolution have led to the emergence of Zn-dependent glycosidases with catalytic proficiency of 2.8 × 10 9 and high β-stereoselectivity. Biochemical characterizations suggest that the Zn-binding site constitutes a key catalytic motif along with at least one adjacent acidic residue. This work demonstrates that unprecedented metalloenzymes can be tailor-made, expanding the scope of inorganic reactivities in proteinaceous environments, resetting the structural and functional diversity of metalloenzymes, and providing the potential molecular basis of unidentified metallohydrolases and novel whole-cell biocatalysts.


  • Organizational Affiliation
    • Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 111.74 kDa 
  • Atom Count: 7,605 
  • Modeled Residue Count: 1,014 
  • Deposited Residue Count: 1,023 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Porin OmpF
A, B, C
341Escherichia coliMutation(s): 0 
Gene Names: ompFD2185_10280
Membrane Entity: Yes 
UniProt
Find proteins for P02931 (Escherichia coli (strain K12))
Explore P02931 
Go to UniProtKB:  P02931
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02931
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.295 (Depositor), 0.302 (DCC) 
  • R-Value Work:  0.269 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 0.271 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.6α = 90
b = 140.39β = 120.01
c = 110.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedKorea, Republic Of2019R1C1C1003863

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references, Structure summary
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description