Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 124125.85 
• Atom Count: 8288 
• Residue Count: 1086 
• Unique protein chains: 1

4XHC

rhamnosidase from Klebsiella oxytoca with rhamnose bound

• DOI: 10.2210/pdb4XHC/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella oxytoca
• Expression System: Escherichia coli


• Deposited: 2015-01-05 Released: 2015-04-15 
• Deposition Author(s): O'Neill, E.O., Stevenson, C.E.M., Patterson, M.J., Rejzek, M., Chauvin, A., Lawson, D.M., Field, R.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council 

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Experimental Data Snapshot

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

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

• PubMed: 25846411 
• 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 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.

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Organizational Affiliation: 

Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.,Laboratorio Nacional De Genómica Para La Biodiversidad (Langebio), CINVESTAV-IPN, Irapuato, Cp36821, México.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Alpha-L-rhamnosidase	A, B	543	Klebsiella oxytoca	Mutation(s): 0  EC: 3.2.1.40
Find proteins for A0A0J9X262 (Klebsiella oxytoca) Go to UniProtKB:  A0A0J9X262

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
RAM	A, B	ALPHA-L-RHAMNOSE C6 H12 O5 SHZGCJCMOBCMKK-HGVZOGFYSA-N

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 = 148.430	α = 90.00
b = 148.430	β = 90.00
c = 202.160	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
SHELX	phasing
PDB_EXTRACT	data extraction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-01-05 
• Released Date: 2015-04-15 
• Deposition Author(s): O'Neill, E.O., Stevenson, C.E.M., Patterson, M.J., Rejzek, M., Chauvin, A., Lawson, D.M., Field, R.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/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