4XHC

rhamnosidase from Klebsiella oxytoca with rhamnose bound

• PDB DOI: https://doi.org/10.2210/pdb4XHC/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella oxytoca
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.70 Å
• R-Value Free: 0.202 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

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: https://doi.org/10.1002/prot.24807
• Primary Citation of Related Structures:  
  4XHC


• 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.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 124.13 kDa 
• Atom Count: 8,333 
• Modelled Residue Count: 1,026 
• Deposited Residue Count: 1,086 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-rhamnosidase	A, B	543	Klebsiella oxytoca	Mutation(s): 0  Gene Names: KOX_19945 EC: 3.2.1.40
UniProt
Find proteins for A0A0J9X262 (Klebsiella oxytoca) Explore A0A0J9X262  Go to UniProtKB:  A0A0J9X262

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAM	C [auth A], F [auth B]	alpha-L-rhamnopyranose C6 H12 O5 SHZGCJCMOBCMKK-HGVZOGFYSA-N
SO4	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.202 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.43	α = 90
b = 148.43	β = 90
c = 202.16	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2015-09-02
  Changes: Database references
• Version 2.0: 2017-08-30
  Changes: Atomic model, Author supporting evidence
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary