4AYO

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.105 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.095 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach.

Thompson, A.J., Dabin, J., Iglesias-Fernandez, J., Ardevol, A., Dinev, Z., Williams, S.J., Bande, O., Siriwardena, A., Moreland, C., Hu, T.C., Smith, D.K., Gilbert, H.J., Rovira, C., Davies, G.J.

(2012) Angew Chem Int Ed Engl 51: 10997

  • DOI: https://doi.org/10.1002/anie.201205338
  • Primary Citation of Related Structures:  
    4AYO, 4AYQ, 4AYR

  • PubMed Abstract: 

    Mannosides in the southern hemisphere: Conformational analysis of enzymatic mannoside hydrolysis informs strategies for enzyme inhibition and inspires solutions to mannoside synthesis. Atomic resolution structures along the reaction coordinate of an inverting α-mannosidase show how the enzyme distorts the substrate and transition state. QM/MM calculations reveal how the free energy landscape of isolated α-D-mannose is molded on enzyme to only allow one conformationally accessible reaction coordinate.

    • Organizational Affiliation: 

    Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE447Caulobacter sp. K31Mutation(s): 0 
EC: 3.2.1.113
UniProt
Find proteins for B0SWV2 (Caulobacter sp. (strain K31))
Explore B0SWV2 
Go to UniProtKB:  B0SWV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0SWV2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.105 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.095 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.77α = 90
b = 143.77β = 90
c = 50.155γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description