6AQY | pdb_00006aqy

Crystal structure of a gdp-l-fucose synthetase from Naegleria fowleri

• PDB DOI: https://doi.org/10.2210/pdb6AQY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Naegleria fowleri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-21 Released: 2017-08-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a gdp-l-fucose synthetase from Naegleria fowleri

Edwards, T.E., Dranow, D.M., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 234.61 kDa 
• Atom Count: 14,671 
• Modeled Residue Count: 1,926 
• Deposited Residue Count: 2,046 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gdp-l-fucose synthetase	A, B, C, D, E, F	341	Naegleria fowleri	Mutation(s): 0  EC: 1.1.1.271
UniProt
Find proteins for A0A2D0TCK0 (Naegleria fowleri) Explore A0A2D0TCK0  Go to UniProtKB:  A0A2D0TCK0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], I [auth B], J [auth C], K [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	H [auth A], L [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36AQY

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.73	α = 90
b = 102.1	β = 107.63
c = 121.82	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-10-22
  Changes: Database references, Structure summary