4XHC

rhamnosidase from Klebsiella oxytoca with rhamnose bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structure of a novel two domain GH78 family alpha-rhamnosidase from Klebsiella oxytoca with rhamnose bound.

O'Neill, E.C.Stevenson, C.E.Paterson, M.J.Rejzek, M.Chauvin, A.L.Lawson, D.M.Field, R.A.

(2015) Proteins 83: 1742-1749

  • DOI: 10.1002/prot.24807

  • PubMed Abstract: 
  • The crystal structure of the GH78 family α-rhamnosidase from Klebsiella oxytoca (KoRha) has been determined at 2.7 Å resolution with rhamnose bound in the active site of the catalytic domain. Curiously, the putative catalytic acid, Asp 222, is preced ...

    The crystal structure of the GH78 family α-rhamnosidase from Klebsiella oxytoca (KoRha) has been determined at 2.7 Å resolution with rhamnose bound in the active site of the catalytic domain. Curiously, the putative catalytic acid, Asp 222, is preceded by an unusual non-proline cis-peptide bond which helps to project the carboxyl group into the active centre. This KoRha homodimeric structure is significantly smaller than those of the other previously determined GH78 structures. Nevertheless, the enzyme displays α-rhamnosidase activity when assayed in vitro, suggesting that the additional structural domains found in the related enzymes are dispensible for function.


    Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-L-rhamnosidase
A, B
543Klebsiella oxytocaMutation(s): 0 
EC: 3.2.1.40
Find proteins for A0A0J9X262 (Klebsiella oxytoca)
Go to UniProtKB:  A0A0J9X262
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
RAM
Query on RAM

Download SDF File 
Download CCD File 
A, B
ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.182 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 148.430α = 90.00
b = 148.430β = 90.00
c = 202.160γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2015-09-02
    Type: Database references
  • Version 2.0: 2017-08-30
    Type: Atomic model, Author supporting evidence