6K1F

Crystal structure of the L-fucose isomerase from Raoultella sp.

• PDB DOI: https://doi.org/10.2210/pdb6K1F/pdb

• Classification: ISOMERASE
• Organism(s): Raoultella planticola
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-10 Released: 2020-05-13 
• Deposition Author(s): Kim, I.J., Kim, D.H., Nam, K.H., Kim, K.H.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.233 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Enzymatic synthesis of l-fucose from l-fuculose using a fucose isomerase fromRaoultellasp. and the biochemical and structural analyses of the enzyme.

Kim, I.J., Kim, D.H., Nam, K.H., Kim, K.H.

(2019) Biotechnol Biofuels 12: 282-282

• PubMed: 31827610 
• DOI: https://doi.org/10.1186/s13068-019-1619-0
• Primary Citation of Related Structures:  
  6K1F, 6K1G


• PubMed Abstract: 
  

  l-Fucose is a rare sugar with potential uses in the pharmaceutical, cosmetic, and food industries. The enzymatic approach using l-fucose isomerase, which interconverts l-fucose and l-fuculose, can be an efficient way of producing l-fucose for industrial applications. Here, we performed biochemical and structural analyses of l-fucose isomerase identified from a novel species of Raoultella ( Rd FucI).

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Organizational Affiliation: 

1Department of Biotechnology, Korea University Graduate School, Seoul, 02841 South Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 404.41 kDa 
• Atom Count: 28,145 
• Modelled Residue Count: 3,522 
• Deposited Residue Count: 3,672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-fucose isomerase	A, B, C, D, E, F	612	Raoultella planticola	Mutation(s): 0  Gene Names: fucI, NCTC13095_01108 EC: 5.3.1.25
UniProt
Find proteins for A0A443VNT1 (Raoultella planticola) Explore A0A443VNT1  Go to UniProtKB:  A0A443VNT1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.233 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.987	α = 90
b = 127.611	β = 90
c = 257.298	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Kim, I.J., Kim, D.H., Nam, K.H., Kim, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description