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 1.1 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: 10.1002/anie.201205338
  • Primary Citation of Related Structures:  
    4AYO, 4AYP, 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASEA447Caulobacter sp. K31Mutation(s): 0 
Gene Names: Caul_4035
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download Ideal Coordinates CCD File 
E [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

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